Methylkit (differential methylation analysis) error in data frame

Methylkit (differential methylation analysis) error in data frame

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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.
    |————————————————–|
    |==================================================|
    Error in [.data.frame(data, , 6) : undefined columns selected


epeigenetics


methylation


differential


analysis


R


methylkit


DNA

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