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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Your attached file is not a .csv file since the field are not separated by commas (just rename the mydata.csv to mydata.txt). The command "genod2 <- as.matrix(genod)" created a character matrix from the data frame genod. When you try to force genod2 to numeric, the marker column becomes NAs which is probably not what you want. The error message is because you passed genod (a data frame) to the snpgdsCreateGeno() function not genod2 (the matrix you created from genod). ------------------------------------ David L. Carlson Department of Anthropology Texas A&M University -----Original Message----- From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of N Meriam Sent: Tuesday, January 8, 2019 1:38 PM To: Michael Dewey <lists at dewey.myzen.co.uk> Cc: r-help at r-project.org Subject: Re: [R] Warning message: NAs introduced by coercion 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
Yes, sorry. I attached the file once again. Well, still getting the same warning.> class(genod) <- "numeric"Warning message: In class(genod) <- "numeric" : NAs introduced by coercion> class(genod)[1] "matrix" Then, I run the following code and it gives this:> 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)> # calculate similarity matrix > # Open the GDS file > (genofile <- snpgdsOpen(filn))File: C:\Users\DELL\Documents\TEST\simTunesian.gds (1.4M) + [ ] * |--+ sample.id { Str8 363 ZIP_ra(42.5%), 755B } |--+ snp.id { Int32 15752 ZIP_ra(35.1%), 21.6K } |--+ snp.position { Int32 15752 ZIP_ra(34.7%), 21.3K } |--+ snp.chromosome { Float64 15752 ZIP_ra(0.18%), 230B } |--+ snp.allele { Str8 15752 ZIP_ra(0.16%), 108B } \--+ genotype { Bit2 15752x363, 1.4M } *> ibs <- snpgdsIBS(genofile, remove.monosnp = FALSE, num.thread=1)Identity-By-State (IBS) analysis on genotypes: Excluding 0 SNP on non-autosomes Working space: 363 samples, 15,752 SNPs using 1 (CPU) core IBS: the sum of all selected genotypes (0,1,2) = 3658952 Tue Jan 08 15:38:00 2019 (internal increment: 42880) [==================================================] 100%, completed in 0s Tue Jan 08 15:38:00 2019 Done.> # maximum similarity value > max(ibs$ibs)[1] NaN> # minimum similarity value > min(ibs$ibs)[1] NaN As you can see, I can't continue my analysis (heat map plot, clustering with hclust) because values are NaN. On Tue, Jan 8, 2019 at 2:01 PM David L Carlson <dcarlson at tamu.edu> wrote:> > Your attached file is not a .csv file since the field are not separated by commas (just rename the mydata.csv to mydata.txt). > > The command "genod2 <- as.matrix(genod)" created a character matrix from the data frame genod. When you try to force genod2 to numeric, the marker column becomes NAs which is probably not what you want. > > The error message is because you passed genod (a data frame) to the snpgdsCreateGeno() function not genod2 (the matrix you created from genod). > > ------------------------------------ > David L. Carlson > Department of Anthropology > Texas A&M University > > -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of N Meriam > Sent: Tuesday, January 8, 2019 1:38 PM > To: Michael Dewey <lists at dewey.myzen.co.uk> > Cc: r-help at r-project.org > Subject: Re: [R] Warning message: NAs introduced by coercion > > 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-- 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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