Hi,
I keep getting errors with importing bismarkCytosine formart bed file. When I check the log, I found all sites have been removed. So I check the source code, and then I found the function rnb.execute.import() line：248 in the file of loading.R has a puzzling parameter, which the function "read.bed.files()" was called with a parameter 'pos.coord.shift=1L,' and an undeclared parameter 'coord.shift = 0L'.
We know the coordinates of Bismark's coverage2cytosine format file are 1-based, so I think the function rnb.execute.import() use the wrong parameter 'pos.coord.shift=1L' , which it should be set 'pos.coord.shift=0L' , When I call read.bed.files() independently use parameter 'pos.coord.shift=0L,', it can read and create an object. So, is it a bug? Please help me to check！
Any help will be highly appreciated.
Thank you.
I use RnBeads 2.40 , The following information may be useful! 1.Below is the parameter pos.coord.shift of function read.bed.files() declaration ： param pos.coord.shift The frame shift between the the CpG annotation (1-based) and the coordinates in the loaded BEDs. If BEDs have 0-based coordinates, \code{pos.coord.shift=1} (default)
2.Below is function rnb.execute.import() line：248 else if (rnb.getOption("import.bed.style")=="bismarkCytosine"){ result <- read.bed.files(base.dir=data.source[[1]], sample.sheet=data.source[[2]], file.names.col=filename.column, verbose=verbose, pos.coord.shift=1L, # I think it should be 0 for (1-based) bed coordinates skip.lines=0, chr.col=1L, start.col=2L, end.col=NA, c.col=4L, t.col=5L, strand.col=3L, mean.meth.col=NA, coverage.col=NA, coord.shift = 0L, # I think it should be remove nrows=nrows)
3. this is part of my wrong log: 2020-03-17 17:47:30 5.2 STATUS STARTED Loading Data From BED Files 2020-03-17 17:47:31 5.2 INFO Reading BED file: .//data//bed/1322P.cytosinereportchr1.bed 2020-03-17 17:47:44 7.6 STATUS Read 1 BED files 2020-03-17 17:47:45 4.0 STATUS Matched chromosomes and strands to annotation 2020-03-17 17:47:45 4.0 STATUS Checked for the presence of sites and coverage 2020-03-17 17:47:45 4.2 STATUS Initialized meth/covg matrices opening ff C:/Users/cby/AppData/Local/Temp/Rtmp0yYQkI/ffb71c4df4595.ff 2020-03-17 17:47:45 4.6 STATUS Combined a data matrix with 4568940 sites and 1 samples 2020-03-17 17:47:45 4.6 STATUS Processed all BED files 2020-03-17 17:47:45 4.6 STATUS STARTED Creating RnBiseqSet object 2020-03-17 17:47:50 5.2 WARNING All sites have been removed, returning NULL 2020-03-17 17:47:50 5.2 STATUS COMPLETED Creating RnBiseqSet object 2020-03-17 17:47:50 5.2 STATUS COMPLETED Loading Data From BED Files 2020-03-17 17:47:50 5.2 STATUS Loaded data from .//data//bed
4. Call read.bed.files() function standalone:
data.source <- c( bedDir , sampleSheet, "filenamebed")
data.source <- as.list(data.source)
result <- read.bed.files(base.dir=data.source[[1]], sample.sheet=data.source[[2]], file.names.col=data.source[[3L]], verbose=TRUE,
pos.coord.shift=0L,
skip.lines=0,
chr.col=1L,
start.col=2L,
end.col=NA,
c.col=4L,
t.col=5L,
strand.col=3L,
mean.meth.col=NA,
coverage.col=NA,
nrows=-1L,
usebigff=TRUE)
Reading BED file: .//data//bed/1322P.cytosinereport_chr1.bed
Read 1 BED files
Matched chromosomes and strands to annotation
Checked for the presence of sites and coverage
Initialized meth/covg matrices
opening ff C:/Users/cby/AppData/Local/Temp/Rtmp0yYQkI/ffb71ca465dd6.ff
Combined a data matrix with 4568940 sites and 1 samples
Processed all BED files
Matched 2284470 of 4568940 methylation sites to the annotation
Checking site coverage
Removed 207795 of 2284470 methylation sites because they were not covered in any sample
Creating methylation matrix
Creating coverage matrix
Creating object
Summarizing strand methylation
Summarizing tiling methylation
Summarizing genes methylation
Summarizing promoters methylation
Summarizing cpgislands methylation
