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al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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Unite function output is methylBase object with 1 row #278

Open fafaris39 opened 1 year ago

fafaris39 commented 1 year ago

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 `

alexg9010 commented 1 year ago

Hi,

A simple reason for the low number of retained CpGs after merging could be that your coverage is too low. Have you checked how many CpGs are retained in each sample? It is possible that the coverage threshold (mincov) of 10 is too high or that one of your samples has low coverage.

Best, Alex