initsWellSamples: Initialising a set of Well samples

In chedonat/DigitalPicoTools: DIGITAL ANALYSIS OF PICOGRAM QUANTITIES OF DNA

Description

This function take as input a vector containing a series of well ID and output of list of WellSample objects corresponding to each well.

Usage

initsWellSamples(WellSamples_list, BAMprefix = NULL, BAMsuffix = NULL,
  unexists.action = "unexists.fail")

Arguments

unexists.action	Define the action to perform when a bam file do not exists. Can be one of the following: unexists.pass No particular action, consider the provided bam file and continue. unexists.fail Interupt the run and generate an error unexists.exclude Do not process the sample, remove it from the list of well and continue The default value is set at unexists.fail
wellSamples_list	a vector of well ID.
Bamprefix	a character string representing a prefix to add to the well ID to match the bam file name in the system file. Should contains the directories making path to the file. Putting the absolute path to the file is recommaeded. default value : empty string.
Bamsuffix	a character string representing a suffix to add after the well_ID in order to match the Bam file name on the file system. This suffux should not include the extemsion '.bam'. Defaults value : empty string

Value

A list of objects of class WellSample

See Also

WellSample

Examples

wellsID_file=system.file('extdata','wells_id_tissue.txt',package='DigitalPicoTools')
 wellsID_list<-unlist(read.table(wellsID_file))
 WellSample_list=initsWellSamples(wellsID_list,
    BAMprefix=paste(path.package('DigitalPicoTools'),'extdata/',sep='/'))
 print(WellSample_list[3])
 # An S4 object of class WellSample
 #
 # Well_ID :  L006
 # Well_Number :  3
 # BAMfilename :  extdata/L006.bam
 #

chedonat/DigitalPicoTools documentation built on May 13, 2019, 3:39 p.m.