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Unite function output is methylBase object with 1 row #278
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Hi, A simple reason for the low number of retained CpGs after merging could be that your coverage is too low. Best, |
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Hello !
I am using unite() function to merge samples but it produced a methylBase object with 1 row, i don't understand where is the problem?!
`
library("methylKit")
file.list = list("/test1-TechRep_1-BioRep_2018.deduplicated.CX_report.txt",
"/test2-TechRep_1-BioRep_2019.deduplicated.CX_report.txt",
"/ctrl1-TechRep_1-BioRep_2018.deduplicated.CX_report.txt",
"/ctrl2-TechRep_1-BioRep_2019.deduplicated.CX_report.txt")
readingReports=methRead(file.list,
sample.id=list("test1","test2","ctrl1","ctrl2"),
assembly="bismark",
treatment=c(1,1,0,0),
context="CpG",
mincov = 10,
pipeline= "bismarkCytosineReport",
dbtype = "tabix",
dbdir = "methylDB"
)
meth=methylKit::unite(readingReports, destrand=FALSE )
head(meth)`
The head of each sample:
`
head ctrl2-TechRep_1-BioRep_2019.deduplicated.CX_report.txt
NC_041792.1 1 + 0 0 CHH CTA
NC_041792.1 5 + 0 0 CHH CCC
NC_041792.1 6 + 0 0 CHH CCT
NC_041792.1 7 + 0 0 CHH CTA
NC_041792.1 12 + 0 0 CHH CCC
head ctrl1-TechRep_1-BioRep_2018.deduplicated.CX_report.txt
NC_041792.1 1 + 0 0 CHH CTA
NC_041792.1 5 + 0 0 CHH CCC
NC_041792.1 6 + 0 0 CHH CCT
NC_041792.1 7 + 0 0 CHH CTA
NC_041792.1 12 + 0 0 CHH CCC
head test1-TechRep_1-BioRep_2018.deduplicated.CX_report.txt
NC_041792.1 1 + 0 0 CHH CTA
NC_041792.1 5 + 0 0 CHH CCC
NC_041792.1 6 + 0 0 CHH CCT
NC_041792.1 7 + 0 0 CHH CTA
NC_041792.1 12 + 0 0 CHH CCC
head test2-TechRep_1-BioRep_2019.deduplicated.CX_report.txt
NC_041792.1 1 + 0 0 CHH CTA
NC_041792.1 5 + 0 0 CHH CCC
NC_041792.1 6 + 0 0 CHH CCT
NC_041792.1 7 + 0 0 CHH CTA
NC_041792.1 12 + 0 0 CHH CCC
`
this is what i got in meth object
`
head(meth)
methylBase object with 1 rows
chr start end strand coverage1 numCs1 numTs1 coverage2 numCs2 numTs2 coverage3 numCs3 numTs3 coverage4 numCs4 numTs4
1 NC_041792.1 16095130 16095130 + 14 0 14 10 0 10 17 2 15 13 0 13
sample.ids: test1 test2 ctrl1 ctrl2
destranded FALSE
assembly: bismark
context: CpG
treament: 1 1 0 0
resolution: base
`
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