checkExtractChipsamples: Check Illumina HT12v4 expression data

In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

Description

This function checks the data and extracts the sample-IDs including information from Illuminas sample-files. See vignette for an example.

Usage

checkExtractChipsamples(
  paramfile = NULL,
  file_names_of_files_and_folders = "from_paramfile",
  colseparator = "from_paramfile",
  renameDublettes = "from_paramfile",
  prefix_new_samplename = "from_paramfile"
)

Arguments

paramfile	Path to the file specifying preprocessing parameters, can be NULL
file_names_of_files_and_folders	Path to a tab-delimeted file with information of files created in Illuminas Genome Studio. Following columns are required: ‘fileset_id': a short ID for a fileset, 'con_f': full path and filename of the control probe data file, 'nobkgd_f': full path and filename of the gene probe data file, 'sample_f': full path and filename of the control probe data file. If NULL, information is used from parameterfile specified in ’paramfile', Default: 'from_paramfile'
colseparator	Separator splitting numbers into units of 1000. Typically "." or ",". Default: 'from_paramfile'
renameDublettes	If any sample Ids is found more than once in the sample file provided by Illumina, suffixes .1 .2 etc are added to the newly created new_ID used to designate samples within the preprocessing. If FALSE, the function will stop when duplicated Sample Ids are found. Default: 'from_paramfile'
prefix_new_samplename	Prefix of new_ID, the new R-compatibel sample names used to designate samples within the preprocessing. Default: 'from_paramfile'

Value

a list of class 'HT12prepro' including a slot with sample-related attributes of the current processing-stage named '$chipsamples'

holgerman/HT12ProcessoR documentation built on June 5, 2021, 9:18 a.m.