Question: Error while using cisAssoc for doing eqtl
0
gravatar for Anupam
2.2 years ago by
Anupam40
CDFD,Hyderabad,India
Anupam40 wrote:

Dear all, I am getting started with eqtl analysis. I have been using this function:

library(GGtools)
library(geuvPack)
data(geuFPKM)
chn<-read.table("gene_list",row.names=FALSE,stringsAsFactors=FALSE,header=TRUE)
gettests = function( chn, useS3=TRUE ) {
library(VariantAnnotation)
snpsp = gtpath( chn$chr, useS3=useS3)
tf = TabixFile( snpsp )
clipped = clipPCs(regressOut(geuFPKM, ~popcode), 1:10)
set.seed(54321)
seqlevelsStyle(clipped) <- "NCBI"
ans = cisAssoc( clipped[ chn$genes, ], tf, cisradius=1000000, lbmaf=0.01 )
metadata(ans)$prepString = "clipPCs(regressOut(geuFPKM, ~popcode), 1:10)"
ans
}

which has been taken from https://www.bioconductor.org/packages/devel/bioc/vignettes/gQTLBase/inst/doc/gQTLBase.html. I get the follwoing error while running cisAssoc function:

Error: subscript is a logical vector with out-of-bounds TRUE values
In addition: Warning message:
In width(ref(v)) == 1 & width(unlist(alt(v))) == 1 :
longer object length is not a multiple of shorter object length

My gene_list file is like this:

chr genes
3       ENSG00000182568.11

Can anyone help me with this ? Thanks in advance.

eqtl ggtools geuvadis • 612 views
ADD COMMENTlink written 2.2 years ago by Anupam40
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