MakeDiploidFSTMat Error X 2

[dani-davenport]

Dear Micheal and Katie

Hoping you could take a look at this issue below and help me out. Got it working, then R crashed, now even after reinstalling the packages and updating still cant get it to work.

FSTmat<- MakeDiploidFSTMat(SNPmat=SNPmat, locusNames=locusNames, popNames=as.character(pops))

Error in tapply(snpDataTemp, list(popNameTemp, snpDataTemp), length) :
arguments must have same length

So we try to transpose matrix... because of conflicting data input information between (a) OUTFLANK readme pdf and ?MakeDiploidFSTMat

SNPmat<- t(SNPmat)

FSTmat<- MakeDiploidFSTMat(SNPmat=SNPmat, locusNames=locusNames, popNames=as.character(pops))
[1] "Error: your population names do not match your SNP matrix"
Error in MakeDiploidFSTMat(SNPmat = SNPmat, locusNames = locusNames, popNames = as.character(pops)) :
no loop for break/next, jumping to top level

Please find attached my genotype data file and locusNames and pops
OutFLANK_data.txt
locusNames_OF.txt
popNames_OF.txt

[DrK-Lo]

Hello, OutFLANK uses a 9 for missing data, as described in the pdf. When I fixed your data, it worked just fine. That is because NAs are removed by the algorithm, resulting in a different length between your vectors. library(OutFLANK) o <- read.table("OUTFLANK_data.txt") dim(o) p <- read.csv("popNames_OF.txt") head(p) l <- read.csv("locusNames_OF.txt") head(l) # Use 9 for missing data sum(is.na(o)) # should not contain NAs o2 <- o o2[is.na(o2)] <- 9 sum(is.na(o2)) dim(o2) levels(factor(as.numeric(unlist(o2)))) out <- MakeDiploidFSTMat(SNPmat=o2, locusNames=l$x, popNames=p$x) out <- MakeDiploidFSTMat(SNPmat=o, locusNames=l$x, popNames=p$x) # replicate error when use NA for missing data

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On Aug 3, 2017, at 1:29 AM, tunaloveheart ***@***.***> wrote: Dear Micheal and Katie Hoping you could take a look at this issue below and help me out. Got it working, then R crashed, now even after reinstalling the packages and updating still cant get it to work. FSTmat<- MakeDiploidFSTMat(SNPmat=SNPmat, locusNames=locusNames, popNames=as.character(pops)) Error in tapply(snpDataTemp, list(popNameTemp, snpDataTemp), length) : arguments must have same length So we try to transpose matrix... because of conflicting data input information between (a) OUTFLANK readme pdf and ?MakeDiploidFSTMat SNPmat<- t(SNPmat) FSTmat<- MakeDiploidFSTMat(SNPmat=SNPmat, locusNames=locusNames, popNames=as.character(pops)) [1] "Error: your population names do not match your SNP matrix" Error in MakeDiploidFSTMat(SNPmat = SNPmat, locusNames = locusNames, popNames = as.character(pops)) : no loop for break/next, jumping to top level Please find attached my genotype data file and locusNames and pops OutFLANK_data.txt <https://github.com/whitlock/OutFLANK/files/1196071/OutFLANK_data.txt> locusNames_OF.txt <https://github.com/whitlock/OutFLANK/files/1196073/locusNames_OF.txt> popNames_OF.txt <https://github.com/whitlock/OutFLANK/files/1196074/popNames_OF.txt> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGjUbYo7aJls_0dAODZBJhyLCDqagoQJks5sUVq6gaJpZM4Or-QX>.

[dani-davenport]

Hey Katie Thanks so much I knew it would be something stupid. When R crashed I mustn't have saved the right data frame which worked the first time because I change the NA to 9. Thanks again and sorry for my stupid question!! Dani

…

Sent from my iPhone

On 3 Aug 2017, at 7:35 pm, Katie Lotterhos ***@***.***> wrote: Hello, OutFLANK uses a 9 for missing data, as described in the pdf. When I fixed your data, it worked just fine. That is because NAs are removed by the algorithm, resulting in a different length between your vectors. library(OutFLANK) o <- read.table("OUTFLANK_data.txt") dim(o) p <- read.csv("popNames_OF.txt") head(p) l <- read.csv("locusNames_OF.txt") head(l) # Use 9 for missing data sum(is.na(o)) # should not contain NAs o2 <- o o2[is.na(o2)] <- 9 sum(is.na(o2)) dim(o2) levels(factor(as.numeric(unlist(o2)))) out <- MakeDiploidFSTMat(SNPmat=o2, locusNames=l$x, popNames=p$x) out <- MakeDiploidFSTMat(SNPmat=o, locusNames=l$x, popNames=p$x) # replicate error when use NA for missing data > On Aug 3, 2017, at 1:29 AM, tunaloveheart ***@***.***> wrote: > > Dear Micheal and Katie > > Hoping you could take a look at this issue below and help me out. Got it working, then R crashed, now even after reinstalling the packages and updating still cant get it to work. > > FSTmat<- MakeDiploidFSTMat(SNPmat=SNPmat, locusNames=locusNames, popNames=as.character(pops)) > > Error in tapply(snpDataTemp, list(popNameTemp, snpDataTemp), length) : > arguments must have same length > > So we try to transpose matrix... because of conflicting data input information between (a) OUTFLANK readme pdf and ?MakeDiploidFSTMat > > SNPmat<- t(SNPmat) > > FSTmat<- MakeDiploidFSTMat(SNPmat=SNPmat, locusNames=locusNames, popNames=as.character(pops)) > [1] "Error: your population names do not match your SNP matrix" > Error in MakeDiploidFSTMat(SNPmat = SNPmat, locusNames = locusNames, popNames = as.character(pops)) : > no loop for break/next, jumping to top level > > Please find attached my genotype data file and locusNames and pops > OutFLANK_data.txt <https://github.com/whitlock/OutFLANK/files/1196071/OutFLANK_data.txt> > locusNames_OF.txt <https://github.com/whitlock/OutFLANK/files/1196073/locusNames_OF.txt> > popNames_OF.txt <https://github.com/whitlock/OutFLANK/files/1196074/popNames_OF.txt> > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub <#7>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGjUbYo7aJls_0dAODZBJhyLCDqagoQJks5sUVq6gaJpZM4Or-QX>. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[saarman]

Thanks I had the same problem. using plink --recodeA gives a genotype matrix with NA, thus this problem. Could you place this conversion of formats [is.na(genotype)] <- 9 in the vignette so that people without a bunch of experience in R can fix their input files to match this non-standard format (i.e. 9 instead of NA)?