Afternoon!
I am having trouble with methylkit read in - I have the methylcall output context files from bismark which I am trying to read into MethylKit. However I am getting the same error after trying to read in as a raw methyl object
Error in fread(filepath, ...) :
Input is either empty or fully whitespace after the skip or autostart. Run again with verbose=TRUE.
library(methylKit)
file.list=list( system.file("extdata",
"CpG_90.txt", package = "methylKit"),
system.file("extdata",
"CpG_91.txt", package = "methylKit"),
system.file("extdata",
"CpG_95.txt", package = "methylKit"),
system.file("extdata",
"CpG_96.txt", package = "methylKit") )
# read the files to a methylRawList object: myobj
myobj=methRead(file.list,
sample.id=list("IN190","IN191","CON95","CON96"),
assembly="onilo11",
treatment=c(1,1,0,0),
context="CpG"
)
I tried adding in the verbose, but it just said it was an unused argument.
Has anyone else had this issue?
Best wishes,
Rebekah
solved - no need for the extra script
file.list=list("CpG_90.txt", "CpG_96.txt")
# read the files to a methylRawList object: myobj
myobj=methRead(file.list,
sample.id=list("IN190","CON96"),
assembly="onilo11",
treatment=c(1,0),
context="CpG"
)
Just read in as above instead