bamToOE: Compute OE scores from (a set of) bamfiles.

In lpagie/chromocounting: Compute OE Scores for Chromocount Experiments

Description

bamToOE computes the observed-over-expected (OE) scores for a set of samples. The input is a bamfile for each sample.

Usage

bamToOE(exp.name, bam.dir = getwd(), bam.fname, sample.name, cell.count,
  sig = sprintf("LP%s", format(Sys.time(), "%y%m%d")), CHR,
  bin.size = 0, fExp, GATC.mpbl.reads, OE.norm.factor = NULL, outdir,
  VERBOSE = FALSE, do.norm = TRUE, plot = TRUE, addToName = "",
  min.depth = 1000, sample.depth = 0L)

Arguments

exp.name	Character, used to create output file names.
bam.dir	Character, directory which contains the bamfiles.
bam.fname	Character vector, bamfile names for all samples.
sample.name	Character vector, (short) names for all samples.
cell.count	Integer vector, cell count for all samples.
sig	Character, string with initials and date used for output file names (eg LP170619).
CHR	Character vector, chromosome names to be used in the analysis.
bin.size	integer, 0 (each bin is entire chr length) or >0 specifying the width in bp of the bins used for computing the OE scores.
fExp	Numeric vector, length of twice the number of GATC fragments in GATC.mpbl.reads (2 reads per fragment) specifying the (normalized) expected readcount per fragment.
GATC.mpbl.reads	GRanges object, granges specify genomic GATC fragments, mcols specifies whether forw/rev/both read count (0/1/2).
OE.norm.factor	Numeric vector, normalization factor per window/chromosome to normalize raw OE scores.
outdir	Character, specifies directory for output files.
VERBOSE	Logical, print diagnostic msgs [default = FALSE].
do.norm	Logical, perform normalization [default = FALSE].
plot	Logical, generate plots [default = TRUE].
addToName	Character, a substrings which will be added in fromt of the chromsome names read from the bamfiles. This allows dealing with bamfiles which lack the 'chr' in the name.
min.depth	integer, minimal read depth per sample (samples with less reads are discarded) [default = 10000].
sample.depth	integer, target read depth per sample (samples will be downsampled to target; must be >= min.depth; sampling is without replacement; set sample.depth to 0 (default) to prevent sampling) [default = 0].

Details

extended description of function

Value

List with 3 elements;

OE.norm.factor

Numeric vector; normalization factor per window/chromosome to normalize raw OE scores

OE.norm

GRanges object; granges specify genomic GATC fragments, mcols specify normalized OE scores for each sample (ie each bamfile)

OE.raw

GRanges object; granges specify genomic GATC fragments, mcols specify raw OE scores for each sample (ie each bamfile)

Examples

## Not run: 
res <- bamToOE(exp.name="myExperiment", bam.dir="./bamfiles/",
  bam.fname=c("1.bam","2.bam"), sample.name=c("smpl1","smpl2"),
  cell.count=c(20,1),CHR=paste0('chr', c(1:19, 'X')), fExp=fExp.mm10,
  GATC.mpbl.reads=GATC.mpbl.reads.mm10, outdir="myResults")

## End(Not run)

lpagie/chromocounting documentation built on May 21, 2019, 2:26 a.m.