I see... Here's a portion of what my data looks like (csv file attached). I run again and here are the results: df4 <- read.csv(file = "mydata.csv", header = TRUE)> require(SNPRelate)> library(gdsfmt)> myd <- df4> myd <- df4> names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25"> myd[,1][1] 3 4 5 6 8 10> # the data must be 0,1,2 with 3 as missing so you have r> sample.id <- names(myd)[-1]> snp.id <- myd[,1]> snp.position <- 1:length(snp.id) # not needed for ibs> snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs> snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs> # genotype data must have - in 3> genod <- myd[,-1]> genod[is.na(genod)] <- 3> genod[genod=="0"] <- 0> genod[genod=="1"] <- 2> genod2 <- as.matrix(genod)> head(genod2) marker X88 X9 X17 X25[1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3" [2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0" [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" [5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3" [6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0"> class(genod2) <- "numeric"Warning message:In class(genod2) <- "numeric" : NAs introduced by coercion> head(genod2)marker X88 X9 X17 X25 [1,] NA 0 3 3 3 [2,] NA 2 0 3 0 [3,] NA 0 0 0 0 [4,] NA 0 0 3 0 [5,] NA 3 3 3 3 [6,] NA 0 0 0 0> class(genod2) <- "numeric"> class(genod2)[1] "matrix"> # read data > filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat = genod,+ sample.id = sample.id, snp.id = snp.id,+ snp.chromosome = snp.chromosome,+ snp.position = snp.position,+ snp.allele = snp.allele, snpfirstdim=TRUE)Error in snpgdsCreateGeno(filn, genmat = genod, sample.id = sample.id, :is.matrix(genmat) is not TRUE Thanks, Meriam On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pikal at precheza.cz> wrote:> Hi > > see in line > > > -----Original Message----- > > From: R-help <r-help-bounces at r-project.org> On Behalf Of N Meriam > > Sent: Tuesday, January 8, 2019 3:08 PM > > To: r-help at r-project.org > > Subject: [R] Warning message: NAs introduced by coercion > > > > Dear all, > > > > I have a .csv file called df4. (15752 obs. of 264 variables). > > I apply this code but couldn't continue further other analyses, a warning > > message keeps coming up. Then, I want to determine max and min > > similarity values, > > heat map plot, cluster...etc > > > > > require(SNPRelate) > > > library(gdsfmt) > > > myd <- read.csv(file = "df4.csv", header = TRUE) > > > names(myd)[-1] > > myd[,1] > > > myd[1:10, 1:10] > > # the data must be 0,1,2 with 3 as missing so you have r > > > sample.id <- names(myd)[-1] > > > snp.id <- myd[,1] > > > snp.position <- 1:length(snp.id) # not needed for ibs > > > snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs > > > snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs > > # genotype data must have - in 3 > > > genod <- myd[,-1] > > > genod[is.na(genod)] <- 3 > > > genod[genod=="0"] <- 0 > > > genod[genod=="1"] <- 2 > > > genod[1:10,1:10] > > > genod <- as.matrix(genod) > > matrix can have only one type of data so you probaly changed it to > character by such construction. > > > > class(genod) <- "numeric" > > This tries to change all "numeric" values to numbers but if it cannot it > sets it to NA. > > something like > > > head(iris) > Sepal.Length Sepal.Width Petal.Length Petal.Width Species > 1 5.1 3.5 1.4 0.2 setosa > 2 4.9 3.0 1.4 0.2 setosa > 3 4.7 3.2 1.3 0.2 setosa > 4 4.6 3.1 1.5 0.2 setosa > 5 5.0 3.6 1.4 0.2 setosa > 6 5.4 3.9 1.7 0.4 setosa > > ir <-head(iris) > > irm <- as.matrix(ir) > > head(irm) > Sepal.Length Sepal.Width Petal.Length Petal.Width Species > 1 "5.1" "3.5" "1.4" "0.2" "setosa" > 2 "4.9" "3.0" "1.4" "0.2" "setosa" > 3 "4.7" "3.2" "1.3" "0.2" "setosa" > 4 "4.6" "3.1" "1.5" "0.2" "setosa" > 5 "5.0" "3.6" "1.4" "0.2" "setosa" > 6 "5.4" "3.9" "1.7" "0.4" "setosa" > > class(irm) <- "numeric" > Warning message: > In class(irm) <- "numeric" : NAs introduced by coercion > > head(irm) > Sepal.Length Sepal.Width Petal.Length Petal.Width Species > 1 5.1 3.5 1.4 0.2 NA > 2 4.9 3.0 1.4 0.2 NA > 3 4.7 3.2 1.3 0.2 NA > 4 4.6 3.1 1.5 0.2 NA > 5 5.0 3.6 1.4 0.2 NA > 6 5.4 3.9 1.7 0.4 NA > > > > Cheers > Petr > > > > > > > > *Warning message:In class(genod) <- "numeric" : NAs introduced by > coercion* > > > > Maybe I could illustrate more with details so I can be more specific? > > Please, let me know. > > > > I would appreciate your help. > > Thanks, > > Meriam > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch > partner? PRECHEZA a.s. jsou zve?ejn?ny na: > https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information > about processing and protection of business partner?s personal data are > available on website: > https://www.precheza.cz/en/personal-data-protection-principles/ > D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou > d?v?rn? a podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? > odpov?dnosti: https://www.precheza.cz/01-dovetek/ | This email and any > documents attached to it may be confidential and are subject to the legally > binding disclaimer: https://www.precheza.cz/en/01-disclaimer/ > >-- *Meriam Nefzaoui* *MSc. in Plant Breeding and Genetics* *Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil*
Dear Meriam Your csv file did not come through as attachments are stripped unless of certain types and you post is very hard to read since you are posting in HTML. Try renaming the file to ????.txt and set your mailer to send plain text then people may be able to help you better. Michael On 08/01/2019 15:35, N Meriam wrote:> I see... > Here's a portion of what my data looks like (csv file attached). > I run again and here are the results: > > df4 <- read.csv(file = "mydata.csv", header = TRUE) > >> require(SNPRelate)> library(gdsfmt)> myd <- df4> myd <- df4> names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25" > >> myd[,1][1] 3 4 5 6 8 10 > > >> # the data must be 0,1,2 with 3 as missing so you have r> sample.id <- names(myd)[-1]> snp.id <- myd[,1]> snp.position <- 1:length(snp.id) # not needed for ibs> snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs> snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs> # genotype data must have - in 3> genod <- myd[,-1]> genod[is.na(genod)] <- 3> genod[genod=="0"] <- 0> genod[genod=="1"] <- 2 > >> genod2 <- as.matrix(genod)> head(genod2) marker X88 X9 X17 X25 > [1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3" > [2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0" > [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" > [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" > [5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3" > [6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0" > >> class(genod2) <- "numeric"Warning message:In class(genod2) <- "numeric" : NAs introduced by coercion> head(genod2) > > marker X88 X9 X17 X25 > [1,] NA 0 3 3 3 > [2,] NA 2 0 3 0 > [3,] NA 0 0 0 0 > [4,] NA 0 0 3 0 > [5,] NA 3 3 3 3 > [6,] NA 0 0 0 0 > >> class(genod2) <- "numeric"> class(genod2)[1] "matrix" > >> # read data > filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat = genod,+ sample.id = sample.id, snp.id = snp.id,+ snp.chromosome = snp.chromosome,+ snp.position = snp.position,+ snp.allele = snp.allele, snpfirstdim=TRUE)Error in snpgdsCreateGeno(filn, genmat = genod, sample.id = sample.id, : > is.matrix(genmat) is not TRUE > > Thanks, > Meriam > > On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pikal at precheza.cz> wrote: > >> Hi >> >> see in line >> >>> -----Original Message----- >>> From: R-help <r-help-bounces at r-project.org> On Behalf Of N Meriam >>> Sent: Tuesday, January 8, 2019 3:08 PM >>> To: r-help at r-project.org >>> Subject: [R] Warning message: NAs introduced by coercion >>> >>> Dear all, >>> >>> I have a .csv file called df4. (15752 obs. of 264 variables). >>> I apply this code but couldn't continue further other analyses, a warning >>> message keeps coming up. Then, I want to determine max and min >>> similarity values, >>> heat map plot, cluster...etc >>> >>>> require(SNPRelate) >>>> library(gdsfmt) >>>> myd <- read.csv(file = "df4.csv", header = TRUE) >>>> names(myd)[-1] >>> myd[,1] >>>> myd[1:10, 1:10] >>> # the data must be 0,1,2 with 3 as missing so you have r >>>> sample.id <- names(myd)[-1] >>>> snp.id <- myd[,1] >>>> snp.position <- 1:length(snp.id) # not needed for ibs >>>> snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs >>>> snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs >>> # genotype data must have - in 3 >>>> genod <- myd[,-1] >>>> genod[is.na(genod)] <- 3 >>>> genod[genod=="0"] <- 0 >>>> genod[genod=="1"] <- 2 >>>> genod[1:10,1:10] >>>> genod <- as.matrix(genod) >> >> matrix can have only one type of data so you probaly changed it to >> character by such construction. >> >>>> class(genod) <- "numeric" >> >> This tries to change all "numeric" values to numbers but if it cannot it >> sets it to NA. >> >> something like >> >>> head(iris) >> Sepal.Length Sepal.Width Petal.Length Petal.Width Species >> 1 5.1 3.5 1.4 0.2 setosa >> 2 4.9 3.0 1.4 0.2 setosa >> 3 4.7 3.2 1.3 0.2 setosa >> 4 4.6 3.1 1.5 0.2 setosa >> 5 5.0 3.6 1.4 0.2 setosa >> 6 5.4 3.9 1.7 0.4 setosa >>> ir <-head(iris) >>> irm <- as.matrix(ir) >>> head(irm) >> Sepal.Length Sepal.Width Petal.Length Petal.Width Species >> 1 "5.1" "3.5" "1.4" "0.2" "setosa" >> 2 "4.9" "3.0" "1.4" "0.2" "setosa" >> 3 "4.7" "3.2" "1.3" "0.2" "setosa" >> 4 "4.6" "3.1" "1.5" "0.2" "setosa" >> 5 "5.0" "3.6" "1.4" "0.2" "setosa" >> 6 "5.4" "3.9" "1.7" "0.4" "setosa" >>> class(irm) <- "numeric" >> Warning message: >> In class(irm) <- "numeric" : NAs introduced by coercion >>> head(irm) >> Sepal.Length Sepal.Width Petal.Length Petal.Width Species >> 1 5.1 3.5 1.4 0.2 NA >> 2 4.9 3.0 1.4 0.2 NA >> 3 4.7 3.2 1.3 0.2 NA >> 4 4.6 3.1 1.5 0.2 NA >> 5 5.0 3.6 1.4 0.2 NA >> 6 5.4 3.9 1.7 0.4 NA >>> >> >> Cheers >> Petr >> >> >>> >>> >>> *Warning message:In class(genod) <- "numeric" : NAs introduced by >> coercion* >>> >>> Maybe I could illustrate more with details so I can be more specific? >>> Please, let me know. >>> >>> I would appreciate your help. >>> Thanks, >>> Meriam >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch >> partner? PRECHEZA a.s. jsou zve?ejn?ny na: >> https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information >> about processing and protection of business partner?s personal data are >> available on website: >> https://www.precheza.cz/en/personal-data-protection-principles/ >> D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou >> d?v?rn? a podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? >> odpov?dnosti: https://www.precheza.cz/01-dovetek/ | This email and any >> documents attached to it may be confidential and are subject to the legally >> binding disclaimer: https://www.precheza.cz/en/01-disclaimer/ >> >> >-- Michael http://www.dewey.myzen.co.uk/home.html
Here's a portion of what my data looks like (text file format attached). When running in R, it gives me this:> df4 <- read.csv(file = "mydata.csv", header = TRUE) > require(SNPRelate) > library(gdsfmt) > myd <- df4 > myd <- df4 > names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25"> myd[,1][1] 3 4 5 6 8 10 # the data must be 0,1,2 with 3 as missing so you have r> sample.id <- names(myd)[-1] > snp.id <- myd[,1] > snp.position <- 1:length(snp.id) # not needed for ibs > snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs > snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs# genotype data must have - in 3> genod <- myd[,-1] > genod[is.na(genod)] <- 3 > genod[genod=="0"] <- 0 > genod[genod=="1"] <- 2 > genod2 <- as.matrix(genod) > head(genod2)marker X88 X9 X17 X25 [1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3" [2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0" [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" [5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3" [6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0"> class(genod2) <- "numeric"Warning message: In class(genod2) <- "numeric" : NAs introduced by coercion> head(genod2)marker X88 X9 X17 X25 [1,] NA 0 3 3 3 [2,] NA 2 0 3 0 [3,] NA 0 0 0 0 [4,] NA 0 0 3 0 [5,] NA 3 3 3 3 [6,] NA 0 0 0 0> class(genod2) <- "numeric" > class(genod2)[1] "matrix" # read data> filn <-"simTunesian.gds" > snpgdsCreateGeno(filn, genmat = genod,+ sample.id = sample.id, snp.id = snp.id, + snp.chromosome = snp.chromosome, + snp.position = snp.position, + snp.allele = snp.allele, snpfirstdim=TRUE) Error in snpgdsCreateGeno(filn, genmat = genod, sample.id = sample.id, : is.matrix(genmat) is not TRUE Can't find a solution to my problem...my guess is that the problem comes from converting the column 'marker' factor to numerical. Best, Meriam On Tue, Jan 8, 2019 at 11:28 AM Michael Dewey <lists at dewey.myzen.co.uk> wrote:> > Dear Meriam > > Your csv file did not come through as attachments are stripped unless of > certain types and you post is very hard to read since you are posting in > HTML. Try renaming the file to ????.txt and set your mailer to send > plain text then people may be able to help you better. > > Michael > > On 08/01/2019 15:35, N Meriam wrote: > > I see... > > Here's a portion of what my data looks like (csv file attached). > > I run again and here are the results: > > > > df4 <- read.csv(file = "mydata.csv", header = TRUE) > > > >> require(SNPRelate)> library(gdsfmt)> myd <- df4> myd <- df4> names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25" > > > >> myd[,1][1] 3 4 5 6 8 10 > > > > > >> # the data must be 0,1,2 with 3 as missing so you have r> sample.id <- names(myd)[-1]> snp.id <- myd[,1]> snp.position <- 1:length(snp.id) # not needed for ibs> snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs> snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs> # genotype data must have - in 3> genod <- myd[,-1]> genod[is.na(genod)] <- 3> genod[genod=="0"] <- 0> genod[genod=="1"] <- 2 > > > >> genod2 <- as.matrix(genod)> head(genod2) marker X88 X9 X17 X25 > > [1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3" > > [2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0" > > [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" > > [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" > > [5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3" > > [6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0" > > > >> class(genod2) <- "numeric"Warning message:In class(genod2) <- "numeric" : NAs introduced by coercion> head(genod2) > > > > marker X88 X9 X17 X25 > > [1,] NA 0 3 3 3 > > [2,] NA 2 0 3 0 > > [3,] NA 0 0 0 0 > > [4,] NA 0 0 3 0 > > [5,] NA 3 3 3 3 > > [6,] NA 0 0 0 0 > > > >> class(genod2) <- "numeric"> class(genod2)[1] "matrix" > > > >> # read data > filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat = genod,+ sample.id = sample.id, snp.id = snp.id,+ snp.chromosome = snp.chromosome,+ snp.position = snp.position,+ snp.allele = snp.allele, snpfirstdim=TRUE)Error in snpgdsCreateGeno(filn, genmat = genod, sample.id = sample.id, : > > is.matrix(genmat) is not TRUE > > > > Thanks, > > Meriam > > > > On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pikal at precheza.cz> wrote: > > > >> Hi > >> > >> see in line > >> > >>> -----Original Message----- > >>> From: R-help <r-help-bounces at r-project.org> On Behalf Of N Meriam > >>> Sent: Tuesday, January 8, 2019 3:08 PM > >>> To: r-help at r-project.org > >>> Subject: [R] Warning message: NAs introduced by coercion > >>> > >>> Dear all, > >>> > >>> I have a .csv file called df4. (15752 obs. of 264 variables). > >>> I apply this code but couldn't continue further other analyses, a warning > >>> message keeps coming up. Then, I want to determine max and min > >>> similarity values, > >>> heat map plot, cluster...etc > >>> > >>>> require(SNPRelate) > >>>> library(gdsfmt) > >>>> myd <- read.csv(file = "df4.csv", header = TRUE) > >>>> names(myd)[-1] > >>> myd[,1] > >>>> myd[1:10, 1:10] > >>> # the data must be 0,1,2 with 3 as missing so you have r > >>>> sample.id <- names(myd)[-1] > >>>> snp.id <- myd[,1] > >>>> snp.position <- 1:length(snp.id) # not needed for ibs > >>>> snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs > >>>> snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs > >>> # genotype data must have - in 3 > >>>> genod <- myd[,-1] > >>>> genod[is.na(genod)] <- 3 > >>>> genod[genod=="0"] <- 0 > >>>> genod[genod=="1"] <- 2 > >>>> genod[1:10,1:10] > >>>> genod <- as.matrix(genod) > >> > >> matrix can have only one type of data so you probaly changed it to > >> character by such construction. > >> > >>>> class(genod) <- "numeric" > >> > >> This tries to change all "numeric" values to numbers but if it cannot it > >> sets it to NA. > >> > >> something like > >> > >>> head(iris) > >> Sepal.Length Sepal.Width Petal.Length Petal.Width Species > >> 1 5.1 3.5 1.4 0.2 setosa > >> 2 4.9 3.0 1.4 0.2 setosa > >> 3 4.7 3.2 1.3 0.2 setosa > >> 4 4.6 3.1 1.5 0.2 setosa > >> 5 5.0 3.6 1.4 0.2 setosa > >> 6 5.4 3.9 1.7 0.4 setosa > >>> ir <-head(iris) > >>> irm <- as.matrix(ir) > >>> head(irm) > >> Sepal.Length Sepal.Width Petal.Length Petal.Width Species > >> 1 "5.1" "3.5" "1.4" "0.2" "setosa" > >> 2 "4.9" "3.0" "1.4" "0.2" "setosa" > >> 3 "4.7" "3.2" "1.3" "0.2" "setosa" > >> 4 "4.6" "3.1" "1.5" "0.2" "setosa" > >> 5 "5.0" "3.6" "1.4" "0.2" "setosa" > >> 6 "5.4" "3.9" "1.7" "0.4" "setosa" > >>> class(irm) <- "numeric" > >> Warning message: > >> In class(irm) <- "numeric" : NAs introduced by coercion > >>> head(irm) > >> Sepal.Length Sepal.Width Petal.Length Petal.Width Species > >> 1 5.1 3.5 1.4 0.2 NA > >> 2 4.9 3.0 1.4 0.2 NA > >> 3 4.7 3.2 1.3 0.2 NA > >> 4 4.6 3.1 1.5 0.2 NA > >> 5 5.0 3.6 1.4 0.2 NA > >> 6 5.4 3.9 1.7 0.4 NA > >>> > >> > >> Cheers > >> Petr > >> > >> > >>> > >>> > >>> *Warning message:In class(genod) <- "numeric" : NAs introduced by > >> coercion* > >>> > >>> Maybe I could illustrate more with details so I can be more specific? > >>> Please, let me know. > >>> > >>> I would appreciate your help. > >>> Thanks, > >>> Meriam > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> ______________________________________________ > >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>> https://stat.ethz.ch/mailman/listinfo/r-help > >>> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >>> and provide commented, minimal, self-contained, reproducible code. > >> Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch > >> partner? PRECHEZA a.s. jsou zve?ejn?ny na: > >> https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information > >> about processing and protection of business partner?s personal data are > >> available on website: > >> https://www.precheza.cz/en/personal-data-protection-principles/ > >> D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou > >> d?v?rn? a podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? > >> odpov?dnosti: https://www.precheza.cz/01-dovetek/ | This email and any > >> documents attached to it may be confidential and are subject to the legally > >> binding disclaimer: https://www.precheza.cz/en/01-disclaimer/ > >> > >> > > > > -- > Michael > http://www.dewey.myzen.co.uk/home.html-- Meriam Nefzaoui MSc. in Plant Breeding and Genetics Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... 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Hm, you should use dput for sharing data but my suggestion was correct. You converted genod to genod2 by as.matrix what changed it to ?character? matrix as matrix is able to hold only one type of data. By trying to change it to numeric, all numbers are changed to numeric and what cannot be changed is simply converted to NA (with polite warning). You should read documentation to snpgdsCreateGeno as it requires matrix as an input and maybe also pay attention to the basic documents like R-intro which would teach you difference between matrix and data frame (chapter 3). Cheers Petr From: N Meriam <meriam.nef at gmail.com> Sent: Tuesday, January 8, 2019 4:36 PM To: PIKAL Petr <petr.pikal at precheza.cz> Cc: r-help at r-project.org Subject: Re: [R] Warning message: NAs introduced by coercion I see... Here's a portion of what my data looks like (csv file attached). I run again and here are the results: df4 <- read.csv(file = "mydata.csv", header = TRUE)> require(SNPRelate)> library(gdsfmt)> myd <- df4> myd <- df4> names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25"> myd[,1][1] 3 4 5 6 8 10> # the data must be 0,1,2 with 3 as missing so you have r> sample.id<http://sample.id> <- names(myd)[-1]> snp.id<http://snp.id> <- myd[,1]> snp.position <- 1:length(snp.id<http://snp.id>) # not needed for ibs> snp.chromosome <- rep(1, each=length(snp.id<http://snp.id>)) # not needed for ibs> snp.allele <- rep("A/G", length(snp.id<http://snp.id>)) # not needed for ibs> # genotype data must have - in 3> genod <- myd[,-1]> genod[is.na<http://is.na>(genod)] <- 3> genod[genod=="0"] <- 0> genod[genod=="1"] <- 2> genod2 <- as.matrix(genod)> head(genod2)marker X88 X9 X17 X25 [1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3" [2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0" [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" [5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3" [6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0"> class(genod2) <- "numeric"Warning message: In class(genod2) <- "numeric" : NAs introduced by coercion> head(genod2)marker X88 X9 X17 X25 [1,] NA 0 3 3 3 [2,] NA 2 0 3 0 [3,] NA 0 0 0 0 [4,] NA 0 0 3 0 [5,] NA 3 3 3 3 [6,] NA 0 0 0 0> class(genod2) <- "numeric"> class(genod2)[1] "matrix"> # read data> filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat = genod,+ sample.id<http://sample.id> = sample.id<http://sample.id>, snp.id<http://snp.id> = snp.id<http://snp.id>, + snp.chromosome = snp.chromosome, + snp.position = snp.position, + snp.allele = snp.allele, snpfirstdim=TRUE) Error in snpgdsCreateGeno(filn, genmat = genod, sample.id<http://sample.id> = sample.id<http://sample.id>, : is.matrix(genmat) is not TRUE Thanks, Meriam On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> wrote: Hi see in line> -----Original Message----- > From: R-help <r-help-bounces at r-project.org<mailto:r-help-bounces at r-project.org>> On Behalf Of N Meriam > Sent: Tuesday, January 8, 2019 3:08 PM > To: r-help at r-project.org<mailto:r-help at r-project.org> > Subject: [R] Warning message: NAs introduced by coercion > > Dear all, > > I have a .csv file called df4. (15752 obs. of 264 variables). > I apply this code but couldn't continue further other analyses, a warning > message keeps coming up. Then, I want to determine max and min > similarity values, > heat map plot, cluster...etc > > > require(SNPRelate) > > library(gdsfmt) > > myd <- read.csv(file = "df4.csv", header = TRUE) > > names(myd)[-1] > myd[,1] > > myd[1:10, 1:10] > # the data must be 0,1,2 with 3 as missing so you have r > > sample.id<http://sample.id> <- names(myd)[-1] > > snp.id<http://snp.id> <- myd[,1] > > snp.position <- 1:length(snp.id<http://snp.id>) # not needed for ibs > > snp.chromosome <- rep(1, each=length(snp.id<http://snp.id>)) # not needed for ibs > > snp.allele <- rep("A/G", length(snp.id<http://snp.id>)) # not needed for ibs > # genotype data must have - in 3 > > genod <- myd[,-1] > > genod[is.na<http://is.na>(genod)] <- 3 > > genod[genod=="0"] <- 0 > > genod[genod=="1"] <- 2 > > genod[1:10,1:10] > > genod <- as.matrix(genod)matrix can have only one type of data so you probaly changed it to character by such construction.> > class(genod) <- "numeric"This tries to change all "numeric" values to numbers but if it cannot it sets it to NA. something like> head(iris)Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa 4 4.6 3.1 1.5 0.2 setosa 5 5.0 3.6 1.4 0.2 setosa 6 5.4 3.9 1.7 0.4 setosa> ir <-head(iris) > irm <- as.matrix(ir) > head(irm)Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 "5.1" "3.5" "1.4" "0.2" "setosa" 2 "4.9" "3.0" "1.4" "0.2" "setosa" 3 "4.7" "3.2" "1.3" "0.2" "setosa" 4 "4.6" "3.1" "1.5" "0.2" "setosa" 5 "5.0" "3.6" "1.4" "0.2" "setosa" 6 "5.4" "3.9" "1.7" "0.4" "setosa"> class(irm) <- "numeric"Warning message: In class(irm) <- "numeric" : NAs introduced by coercion> head(irm)Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 NA 2 4.9 3.0 1.4 0.2 NA 3 4.7 3.2 1.3 0.2 NA 4 4.6 3.1 1.5 0.2 NA 5 5.0 3.6 1.4 0.2 NA 6 5.4 3.9 1.7 0.4 NA>Cheers Petr> > > *Warning message:In class(genod) <- "numeric" : NAs introduced by coercion* > > Maybe I could illustrate more with details so I can be more specific? > Please, let me know. > > I would appreciate your help. > Thanks, > Meriam > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch partner? PRECHEZA a.s. jsou zve?ejn?ny na: https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about processing and protection of business partner?s personal data are available on website: https://www.precheza.cz/en/personal-data-protection-principles/ D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? odpov?dnosti: https://www.precheza.cz/01-dovetek/ | This email and any documents attached to it may be confidential and are subject to the legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/ -- Meriam Nefzaoui MSc. in Plant Breeding and Genetics Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil [[alternative HTML version deleted]]
And as you use bioconductor related package you probably could get better answers in specialised biconductor help https://www.bioconductor.org/help/ Cheers Petr From: N Meriam <meriam.nef at gmail.com> Sent: Tuesday, January 8, 2019 4:36 PM To: PIKAL Petr <petr.pikal at precheza.cz> Cc: r-help at r-project.org Subject: Re: [R] Warning message: NAs introduced by coercion I see... Here's a portion of what my data looks like (csv file attached). I run again and here are the results: df4 <- read.csv(file = "mydata.csv", header = TRUE)> require(SNPRelate)> library(gdsfmt)> myd <- df4> myd <- df4> names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25"> myd[,1][1] 3 4 5 6 8 10> # the data must be 0,1,2 with 3 as missing so you have r> sample.id<http://sample.id> <- names(myd)[-1]> snp.id<http://snp.id> <- myd[,1]> snp.position <- 1:length(snp.id<http://snp.id>) # not needed for ibs> snp.chromosome <- rep(1, each=length(snp.id<http://snp.id>)) # not needed for ibs> snp.allele <- rep("A/G", length(snp.id<http://snp.id>)) # not needed for ibs> # genotype data must have - in 3> genod <- myd[,-1]> genod[is.na<http://is.na>(genod)] <- 3> genod[genod=="0"] <- 0> genod[genod=="1"] <- 2> genod2 <- as.matrix(genod)> head(genod2)marker X88 X9 X17 X25 [1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3" [2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0" [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" [5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3" [6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0"> class(genod2) <- "numeric"Warning message: In class(genod2) <- "numeric" : NAs introduced by coercion> head(genod2)marker X88 X9 X17 X25 [1,] NA 0 3 3 3 [2,] NA 2 0 3 0 [3,] NA 0 0 0 0 [4,] NA 0 0 3 0 [5,] NA 3 3 3 3 [6,] NA 0 0 0 0> class(genod2) <- "numeric"> class(genod2)[1] "matrix"> # read data> filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat = genod,+ sample.id<http://sample.id> = sample.id<http://sample.id>, snp.id<http://snp.id> = snp.id<http://snp.id>, + snp.chromosome = snp.chromosome, + snp.position = snp.position, + snp.allele = snp.allele, snpfirstdim=TRUE) Error in snpgdsCreateGeno(filn, genmat = genod, sample.id<http://sample.id> = sample.id<http://sample.id>, : is.matrix(genmat) is not TRUE Thanks, Meriam On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> wrote: Hi see in line> -----Original Message----- > From: R-help <r-help-bounces at r-project.org<mailto:r-help-bounces at r-project.org>> On Behalf Of N Meriam > Sent: Tuesday, January 8, 2019 3:08 PM > To: r-help at r-project.org<mailto:r-help at r-project.org> > Subject: [R] Warning message: NAs introduced by coercion > > Dear all, > > I have a .csv file called df4. (15752 obs. of 264 variables). > I apply this code but couldn't continue further other analyses, a warning > message keeps coming up. Then, I want to determine max and min > similarity values, > heat map plot, cluster...etc > > > require(SNPRelate) > > library(gdsfmt) > > myd <- read.csv(file = "df4.csv", header = TRUE) > > names(myd)[-1] > myd[,1] > > myd[1:10, 1:10] > # the data must be 0,1,2 with 3 as missing so you have r > > sample.id<http://sample.id> <- names(myd)[-1] > > snp.id<http://snp.id> <- myd[,1] > > snp.position <- 1:length(snp.id<http://snp.id>) # not needed for ibs > > snp.chromosome <- rep(1, each=length(snp.id<http://snp.id>)) # not needed for ibs > > snp.allele <- rep("A/G", length(snp.id<http://snp.id>)) # not needed for ibs > # genotype data must have - in 3 > > genod <- myd[,-1] > > genod[is.na<http://is.na>(genod)] <- 3 > > genod[genod=="0"] <- 0 > > genod[genod=="1"] <- 2 > > genod[1:10,1:10] > > genod <- as.matrix(genod)matrix can have only one type of data so you probaly changed it to character by such construction.> > class(genod) <- "numeric"This tries to change all "numeric" values to numbers but if it cannot it sets it to NA. something like> head(iris)Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa 4 4.6 3.1 1.5 0.2 setosa 5 5.0 3.6 1.4 0.2 setosa 6 5.4 3.9 1.7 0.4 setosa> ir <-head(iris) > irm <- as.matrix(ir) > head(irm)Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 "5.1" "3.5" "1.4" "0.2" "setosa" 2 "4.9" "3.0" "1.4" "0.2" "setosa" 3 "4.7" "3.2" "1.3" "0.2" "setosa" 4 "4.6" "3.1" "1.5" "0.2" "setosa" 5 "5.0" "3.6" "1.4" "0.2" "setosa" 6 "5.4" "3.9" "1.7" "0.4" "setosa"> class(irm) <- "numeric"Warning message: In class(irm) <- "numeric" : NAs introduced by coercion> head(irm)Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 NA 2 4.9 3.0 1.4 0.2 NA 3 4.7 3.2 1.3 0.2 NA 4 4.6 3.1 1.5 0.2 NA 5 5.0 3.6 1.4 0.2 NA 6 5.4 3.9 1.7 0.4 NA>Cheers Petr> > > *Warning message:In class(genod) <- "numeric" : NAs introduced by coercion* > > Maybe I could illustrate more with details so I can be more specific? > Please, let me know. > > I would appreciate your help. > Thanks, > Meriam > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch partner? PRECHEZA a.s. jsou zve?ejn?ny na: https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about processing and protection of business partner?s personal data are available on website: https://www.precheza.cz/en/personal-data-protection-principles/ D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? odpov?dnosti: https://www.precheza.cz/01-dovetek/ | This email and any documents attached to it may be confidential and are subject to the legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/ -- Meriam Nefzaoui MSc. in Plant Breeding and Genetics Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil [[alternative HTML version deleted]]