CS.Process: Normalize CytoScanHD_Array arrays using Affymetrix Power...

Description Usage Arguments Details Author(s)

View source: R/apt_cytoscan_process.R

Description

This function performs the normalization of a CEL file of Affymetrix CytoScanHD_Array microarray using the APT binary (apt-copynumber-cyto).

Usage

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CS.Process(CEL = NULL, samplename = NULL, dual.norm = FALSE,
normal.diploid = FALSE, l2r.level = "weighted", gc.renorm = TRUE,
gc.rda = NULL, wave.renorm = TRUE, wave.rda = NULL,
mingap = 1E+06, out.dir = getwd(), oschp.keep = FALSE, force.OS =
NULL, apt.version = "2.4.0", apt.build = "na33.r4", genome.pkg =
"BSgenome.Hsapiens.UCSC.hg19", return.data = FALSE, write.data = 
TRUE, plot = TRUE, force = FALSE) 

Arguments

CEL

A CEL file.

samplename

Name of the analyzed sample.

dual.norm

Perform a dual-channel normalization (recommended for a better wave-effect bias normalization).

normal.diploid

Consider the sample as normal-diploid (not recommended for tumors).

l2r.level

Type of log2(ratio) to extract : 'weighted' or 'normal'.

gc.renorm

Perform a 'GC-content' re-normalization after APT processing.

gc.rda

If gc.renorm set to TRUE, specifies the data package containing GC-content tracks. If NULL, a default one (included in the affy.CN.norm.data package) will be used.

wave.renorm

Perform a 'Wave-effect' re-normalization after APT processing.

wave.rda

If wave.renorm set to TRUE, specifies the data package containing Wave tracks. If NULL, a default one (included in the affy.CN.norm.data package) will be used.

mingap

Minimum genomic size to be considered as an uncovered gap in the design (allows to discard centromeres).

out.dir

The path to output results.

oschp.keep

Keep the intermediate OSCHP (HDF5) file.

force.OS

Specifiy the OS type of the execution machine (see Details).

apt.version

Version of the APT tool apt-copynumber-cyto.

apt.build

Affymetrix genome build version.

genome.pkg

The name of an installed BSgenome package. Please verify that provided package is compatible with the provided apt.build genome version.

return.data

Return data when finished.

write.data

Write the results as a RDS file.

plot

Perform plots.

force

If some result files already exist, delete them before runing.

Details

force.OS is NULL by default, but can take any of these values :

Author(s)

Bastien Job


gustaveroussy/EaCoN documentation built on Oct. 20, 2021, 2:41 a.m.