inputfille
snpid indid genotype gvariable probeid gene geneexpression
rs1040480 CHB_NA18524 C/T 2 GI_19743926-I PTPRT 5.850586
rs1040480 CHB_NA18526 C/C 1 GI_19743926-I PTPRT 6.028641
rs1040480 CHB_NA18529 C/C 3 GI_19743926-I PTPRT 5.944392
rs1040481 CHB_NA18532 C/C 1 GI_19743926-I PTPRT 5.938578
rs1040481 CHB_NA18537 C/C 2 GI_19743926-I PTPRT 5.874439
rs1040481 CHB_NA18540 C/C 3 GI_19743926-I PTPRT 5.915231
output
rs1040480 pvalue:0.39 or something like that
rs1040481 pvalue:0.02...
error
Error in pf(q, df1, df2, lower.tail, log.p) :
Non-numeric argument to mathematical function
script I'm using
data1<-read.table("C:\\Documents and
Settings\\bogugk\\Desktop\\Update_Rory\\A_G_without_NN_Results.txt",
header=TRUE)
fm <- lmList(geneexpression~gvariable|snpid,data=data1)
get.pval <- function(z) {
x <- summary(z)
pf(x$fstatistic[1L], x$fstatistic[2L], x$fstatistic[3L], lower.tail =
FALSE)
}
sapply(fm,get.pval)
Needed output
snpid gene pvalue
rs1040480 PTPRT 0.39
rs1040481 PTPRT 0.02
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