champ.load_extended: Modified champ.load function from the _ChAMP_ package

In LionelRohner/LRTools: A collection of functions written for analyzing Illumina HM450 and EPIC data

Description

This is a modification of the function "champ.load" from the ChAMP package, which allows to use the Noob background correction. The original function from ChAMP loads data from IDAT files to calculate intensity and produce quality control images. Furthermore, a new argument has been added that allows to load a specific sample sheet using a regular expression. This avoids the errors of the normal loading function when multiple csv files are found in the working directory. Only the new arguments are presented here. The other arguments can be found in the ChAMP manual here: https://rdrr.io/bioc/ChAMP/man/champ.load.html. The modification are minor, see line 94 and 104 to 111, everything else is from the ChAMP package created by Yuan Tian (cre,aut), Tiffany Morris (ctb), Lee Stirling (ctb), Andrew Feber (ctb), Andrew Teschendorff (ctb), Ankur Chakravarthy (ctb). ChAMP is licensed under GPL-3.

Usage

champ.load_extended(
  directory = getwd(),
  method = "ChAMP",
  methValue = "B",
  autoimpute = TRUE,
  filterDetP = TRUE,
  ProbeCutoff = 0,
  SampleCutoff = 0.1,
  detPcut = 0.01,
  filterBeads = TRUE,
  beadCutoff = 0.05,
  filterNoCG = TRUE,
  filterSNPs = TRUE,
  population = NULL,
  filterMultiHit = TRUE,
  filterXY = TRUE,
  force = FALSE,
  arraytype = "450K",
  sampleSheet.csv = "csv$",
  preproc = "Noob",
  dyeMethod = "single"
)

Arguments

directory	See ChAMP manual.
method	See ChAMP manual.
methValue	See ChAMP manual.
autoimpute	See ChAMP manual.
filterDetP	See ChAMP manual.
ProbeCutoff	See ChAMP manual.
SampleCutoff	See ChAMP manual.
detPcut	See ChAMP manual.
filterBeads	See ChAMP manual.
beadCutoff	See ChAMP manual.
filterNoCG	See ChAMP manual.
filterSNPs	See ChAMP manual.
population	See ChAMP manual.
filterMultiHit	See ChAMP manual.
filterXY	See ChAMP manual.
force	See ChAMP manual.
arraytype	See ChAMP manual.
sampleSheet.csv	An optional argument, that allows to add the name of a specific sample sheet using regular expressions.
preproc	Choice of the preprocessing method of the rgSet. To use Noob dye bias and background correction use "Noob". The function is available in the minfi package. Using "Raw" is the standard ChAMP method and does not include background correction.
dyeMethod	To date single sample procedure of Noob ("single") is the only choice here.

Value

A list including the rgSet, mSet, beta-value matrix, detection p-value matrix, and a matrix of intensity values. See ChAMP manual for more detail.

Examples

## Not run: myLoad_450K <- champ.load_extended(method = "minfi",
                                 arraytype = "450K",
                                 sampleSheet.csv ="^someSampleSheet.csv$",
                                 preproc = "Noob",
                                 dyeMethod = "single")
## End(Not run)

LionelRohner/LRTools documentation built on Dec. 17, 2021, 1:10 a.m.