madseqloy: Check the loss of Y events in a given folder of .bam files

Description Usage Arguments Value Examples

View source: R/MADseqLOY.R

Description

MADseqLOY check all the bams in a given folder, by using the target regions of the technology used to sequence the sample. The coverage is computed for the region chrY:2694521-59034049 (hg19/GRCh37) and another given by the ref.region argument.

Usage

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madseqloy(files, exomeTargets, target.region = "chrY:2694521-59034049",
  ref.region = "chr22", mc.cores, quiet = FALSE, skip = 2, ...)

Arguments

files

A folder path where the .bam files are or a vector of file paths. This function searches in recursive folders.

exomeTargets

A file path to a .bed file with the regions targeted by the sequencing method used.

target.region

The chromosome or region to be compared with the other regions. By default is the region chrY:2694521-59034049 but it can be changed.

ref.region

First chromosome or region to be compared with the Y region in UCSC style (i.e. "chr22" or "chr21:1000-10000").

mc.cores

umber of cores to be used with this function. If there are more cores than samples, the number of cores will be limited to the number of samples. By default set to 1.

quiet

Should the function not inform about the status of the process. By default is FALSE.

skip

Number of lines to be skipped in the targets file if necessary. By default is set to 1.

...

Other parameters of the read.targets function.

Value

The returned value is an object of "MADseqLOY" class with three lists, one regarding the target region coverage called "target", another regarding the reference regions to be compared against called "reference" and finally one with the parameters used in the query.

Examples

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## Not run: 
madseqloy(files=bamFile, reference=targetFile, skip=0)
## End(Not run)

isglobal-brge/MADloy documentation built on June 11, 2017, 2:40 a.m.