Hello, I would like to use this package metap to calculate multiple o values I have my data frame with 3 p values> head(tt)RS G E B 1: rs2089177 0.9986 0.7153 0.604716 2: rs4360974 0.9738 0.7838 0.430228 3: rs6502526 0.9744 0.7839 0.429160 4: rs8069906 0.7184 0.4918 0.521452 5: rs9905280 0.7205 0.4861 0.465758 6: rs4313843 0.9804 0.8522 0.474313 and data frame with corresponding weights for each of the p values from the tt data frame> head(df)wg we wb RS 1 40.6325 35.39774 580.6436 rs2089177 2 40.6325 35.39774 580.6436 rs4360974 3 40.6325 35.39774 580.6436 rs6502526 4 40.6325 35.39774 580.6436 rs8069906 5 40.6325 35.39774 580.6436 rs9905280 6 40.6325 35.39774 580.6436 rs4313843 RS column is the same in df and tt How to use this sunz() function to create a new data frame which would look the same as tt only it would have additional column, say named "META" which has calculated meta p values for each row This i s example of how much would be p value in the first row:> sumz(c(0.9986,0.7153,0.604716), weights = c(40.6325,35.39774,580.6436), na.action = na.fail)p = 0.6940048 Thanks Ana
this is the function I was referring to: https://www.rdocumentation.org/packages/metap/versions/1.1/topics/sumz On Fri, Oct 25, 2019 at 6:31 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:> > Hello, > > I would like to use this package metap > to calculate multiple o values > > I have my data frame with 3 p values > > head(tt) > RS G E B > 1: rs2089177 0.9986 0.7153 0.604716 > 2: rs4360974 0.9738 0.7838 0.430228 > 3: rs6502526 0.9744 0.7839 0.429160 > 4: rs8069906 0.7184 0.4918 0.521452 > 5: rs9905280 0.7205 0.4861 0.465758 > 6: rs4313843 0.9804 0.8522 0.474313 > > and data frame with corresponding weights for each of the p values > from the tt data frame > > > head(df) > wg we wb RS > 1 40.6325 35.39774 580.6436 rs2089177 > 2 40.6325 35.39774 580.6436 rs4360974 > 3 40.6325 35.39774 580.6436 rs6502526 > 4 40.6325 35.39774 580.6436 rs8069906 > 5 40.6325 35.39774 580.6436 rs9905280 > 6 40.6325 35.39774 580.6436 rs4313843 > > RS column is the same in df and tt > > How to use this sunz() function to create a new data frame which would > look the same as tt only it would have additional column, say named > "META" which has calculated meta p values for each row > > This i s example of how much would be p value in the first row: > > > sumz(c(0.9986,0.7153,0.604716), weights = c(40.6325,35.39774,580.6436), na.action = na.fail) > p = 0.6940048 > > Thanks > Ana
Dear Ana There must be several ways of doing this but see below for an idea with comments in-line. On 26/10/2019 00:31, Ana Marija wrote:> Hello, > > I would like to use this package metap > to calculate multiple o values > > I have my data frame with 3 p values >> head(tt) > RS G E B > 1: rs2089177 0.9986 0.7153 0.604716 > 2: rs4360974 0.9738 0.7838 0.430228 > 3: rs6502526 0.9744 0.7839 0.429160 > 4: rs8069906 0.7184 0.4918 0.521452 > 5: rs9905280 0.7205 0.4861 0.465758 > 6: rs4313843 0.9804 0.8522 0.474313 > > and data frame with corresponding weights for each of the p values > from the tt data frame > >> head(df) > wg we wb RS > 1 40.6325 35.39774 580.6436 rs2089177 > 2 40.6325 35.39774 580.6436 rs4360974 > 3 40.6325 35.39774 580.6436 rs6502526 > 4 40.6325 35.39774 580.6436 rs8069906 > 5 40.6325 35.39774 580.6436 rs9905280 > 6 40.6325 35.39774 580.6436 rs4313843 > > RS column is the same in df and tt >So you can create a new data-frame with merge() newdata <- merge(tt, df) which will use RS as the key to merge them on. The write a function of one argument, a seven element vector, which picks out the p-values and the weights and feeds them to sumz(). Something like helper <- function(x) { p <- sumz(x[2:4], weights = x[5:7])$p p } Note you need to check that 2:4 and 5:7 are actually where they are in the row of newdat. Then use apply() to apply that to the rows of newdat. I have not tested any of this but the general idea should be OK even if the details are wrong. Michael> How to use this sunz() function to create a new data frame which would > look the same as tt only it would have additional column, say named > "META" which has calculated meta p values for each row > > This i s example of how much would be p value in the first row: > >> sumz(c(0.9986,0.7153,0.604716), weights = c(40.6325,35.39774,580.6436), na.action = na.fail) > p = 0.6940048 > > Thanks > Ana > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Michael http://www.dewey.myzen.co.uk/home.html
Hi Michael, I tried what you proposed with my data frame q:> head(q)ID P G E wb wg we 1: rs1029830 0.0979931 0.0054060 0.39160 580.6436 40.6325 35.39774 2: rs1029832 0.1501820 0.0028140 0.39320 580.6436 40.6325 35.39774 3: rs11078374 0.1701250 0.0009805 0.49730 580.6436 40.6325 35.39774 4: rs1124961 0.1710150 0.7252000 0.05737 580.6436 40.6325 35.39774 5: rs1135237 0.1493650 0.6851000 0.06354 580.6436 40.6325 35.39774 6: rs11867934 0.0757972 0.0006140 0.00327 580.6436 40.6325 35.39774 so the solution of the first row would be this:> sumz(c(0.0979931,0.0054060,0.39160), weights = c(580.6436,40.6325,35.39774), na.action = na.fail)sumz = 1.481833 p = 0.06919239 I tried applying the function you wrote: helper <- function(x) { p <- sumz(x[2:4], weights = x[5:7])$p p } With: q$META <- apply(q, MARGIN = 1, helper) # I want to make a new column in q named META with results but I got this error: Error in sumz(x[2:4], weights = x[5:7]) : Must have at least two valid p values Please advise, Ana On Sun, Oct 27, 2019 at 9:49 AM Michael Dewey <lists at dewey.myzen.co.uk> wrote:> > Dear Ana > > There must be several ways of doing this but see below for an idea with > comments in-line. > > On 26/10/2019 00:31, Ana Marija wrote: > > Hello, > > > > I would like to use this package metap > > to calculate multiple o values > > > > I have my data frame with 3 p values > >> head(tt) > > RS G E B > > 1: rs2089177 0.9986 0.7153 0.604716 > > 2: rs4360974 0.9738 0.7838 0.430228 > > 3: rs6502526 0.9744 0.7839 0.429160 > > 4: rs8069906 0.7184 0.4918 0.521452 > > 5: rs9905280 0.7205 0.4861 0.465758 > > 6: rs4313843 0.9804 0.8522 0.474313 > > > > and data frame with corresponding weights for each of the p values > > from the tt data frame > > > >> head(df) > > wg we wb RS > > 1 40.6325 35.39774 580.6436 rs2089177 > > 2 40.6325 35.39774 580.6436 rs4360974 > > 3 40.6325 35.39774 580.6436 rs6502526 > > 4 40.6325 35.39774 580.6436 rs8069906 > > 5 40.6325 35.39774 580.6436 rs9905280 > > 6 40.6325 35.39774 580.6436 rs4313843 > > > > RS column is the same in df and tt > > > > So you can create a new data-frame with merge() > > newdata <- merge(tt, df) > > which will use RS as the key to merge them on. > > The write a function of one argument, a seven element vector, which > picks out the p-values and the weights and feeds them to sumz(). > Something like > > helper <- function(x) { > p <- sumz(x[2:4], weights = x[5:7])$p > p > } > Note you need to check that 2:4 and 5:7 are actually where they are in > the row of newdat. > > Then use apply() to apply that to the rows of newdat. > > I have not tested any of this but the general idea should be OK even if > the details are wrong. > > Michael > > > > How to use this sunz() function to create a new data frame which would > > look the same as tt only it would have additional column, say named > > "META" which has calculated meta p values for each row > > > > This i s example of how much would be p value in the first row: > > > >> sumz(c(0.9986,0.7153,0.604716), weights = c(40.6325,35.39774,580.6436), na.action = na.fail) > > p = 0.6940048 > > > > Thanks > > Ana > > > > ______________________________________________ > > 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. > > > > -- > Michael > http://www.dewey.myzen.co.uk/home.html