EaCoN: EaCoN : Easy Copy Number !

Description Usage Arguments Details Author(s)

This function performs the normalization of a CEL file pair of Affymetrix OncoScan or OncoScan_CNV microarray using the APT binary (apt-copynumber-onco-ssa).

OS.Process(ATChannelCel = NULL, GCChannelCel = NULL, samplename =
NULL, dual.norm = TRUE, 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.r2", genome.pkg =
"BSgenome.Hsapiens.UCSC.hg19", return.data = FALSE, write.data = TRUE,
plot = TRUE, force = FALSE)

`ATChannelCel`	The first CEL file (version A).
`GCChannelCel`	The second CEL file (version C).
`samplename`	Name of the analyzed sample.
`dual.norm`	Perform a dual-channel normalization (recommended for a better wave-effect bias normalization).
`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.