cnv_readprofile: Read copy number as a list of data.frame from data.frame or...

In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description

This function is used to read copy number profile for preparing CNV signature analysis.

Usage

cnv_readprofile(input, is_dir = FALSE, pattern = NULL,
  ignore_case = FALSE, sep = "\t", cols = c("Chromosome",
  "Start.bp", "End.bp", "modal_cn"), have_sampleCol = TRUE,
  sample_col = "sample")

Arguments

input	a data.frame or a file or a directory contains copy number profile.
is_dir	logical. Is input a directory?
pattern	an optional regular expression used to select part of files if input is a directory, more detail please see list.files function.
ignore_case	logical. Should pattern-matching be case-insensitive?
sep	the field separator character for input file(s) if input is not data.frame.
cols	four characters used to specify chromosome, start position, end position and copy number value in input, respectively. Default use names from ABSOLUTE calling result.
have_sampleCol	logical. Does input have sample column? This parameter must be TRUE and sample_col also properly be assigned when input is a file or a data.frame (i.e. not a directory).
sample_col	a character used to specify the sample column name.

Value

a list contains absolute copy-number profile for multiple samples.

Author(s)

Shixiang Wang [e-mail]

See Also

cnv_derivefeatures() for deriving CNV features, cnv_getLengthFraction() for calculating CNV length fraction (normalized to arm), cnv_plotDistributionProfile() for plotting profile of CNV distribution.

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_extractSignatures, cnv_fitMixModels, cnv_generateSbCMatrix, cnv_getLengthFraction, cnv_pipe, cnv_plotDistributionProfile, cnv_plotFeatureDistribution, cnv_plotMixComponents, cnv_plotSignatures, cnv_quantifySigExposure

ShixiangWang/VSHunter documentation built on June 27, 2019, 4:56 p.m.