Methread() function problem

Question

[Mireia]

Hello,

Recently I received methylation call files from my last RRBS and RRoxBS analysis and I would like to analyse them with the Methylkit R package.

I have executed the next script:

WT8_BS <- read_table("T:/RROxBS/WT8_BS/methylcall.CpG.WT8_BS.1x.txt", col_names = FALSE)
KO8_BS <- read_table("T:/RROxBS/KO8_BS/methylcall.CpG.KO8_BS.1x.txt", col_names = FALSE)
WT8_BS <- select(WT8_BS, -X8, -X9)
KO8_BS <- select(KO8_BS, -X8, -X9)

names(WT8_BS) <- c("chrBase", "chr", "base", "strand", "coverage", "freqC", "freqT")
names(KO8_BS) <- c("chrBase", "chr", "base", "strand", "coverage", "freqC", "freqT")

files <- list(WT8_BS, KO8_BS)

WT8 <- methRead(files, 
                sample.id = list("WT8_BS", "KO8_BS"),
                assembly = "mm10",
                treatment = c(0,1),
                context = "CpG",
                dbtype = "tabix",
                dbdir = "methylDB"
                )

My problem is that when I execute the last step it never ends, it remains like the image:

I do not know which could be the problem. I also tried to read the methylation call files and store them as flat file database as it says in mehtylkit manual, but it does not work either.

Thanks in advance!

Answer 1

[Basti]

files should be a list of locations instead of imported dataset :

files = list("T:/RROxBS/WT8_BS/methylcall.CpG.WT8_BS.1x.txt","T:/RROxBS/KO8_BS/methylcall.CpG.KO8_BS.1x.txt")

[Mireia]

Thank you! It was the problem!