Methylkit (differential methylation analysis) error in data frame
Hi Friends,
I am performing the differential methylation analysis using methylkit but it is throwing error in data frame. ” Error in [.data.frame
(data, , 6) : undefined columns selected”. Can anyone help me to solve this error. Following is my R cmmand lnes. Thanks
Raj
library(methylKit)
library(methylKit)
file.list=list( “CpG_context_ST12_B1_F_bismark_hisat2_pe.txt”,”CpG_context_ST12_B2_F_bismark_hisat2_pe.txt”,”CpG_context_ST12_B3_F_bismark_hisat2_pe.txt”,”CpG_context_ST2_B1_F_bismark_hisat2_pe.txt”,”CpG_context_ST2_B2_F_bismark_hisat2_pe.txt”,”CpG_context_ST2_B3_F_bismark_hisat2_pe.txt”)myobj=methRead(file.list,
- sample.id=list(“test1″,”test2″,”test3″,”ctrl1″,”ctrl2″,”ctrl3”),
- assembly=”Edwards”,
- treatment=c(1,1,1,0,0,0),
- context=”CpG”,
- mincov = 10,
- pipeline = “bismark”
- )
Received list of locations.
Reading file.
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Error in[.data.frame
(data, , 6) : undefined columns selected
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