loadCNVcalls: loadCNVcalls

In CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

Description

Loads CNV calls from a csv/tsv file

Usage

loadCNVcalls(
  cnvs.file,
  chr.column,
  start.column,
  end.column,
  coord.column = NULL,
  cnv.column,
  sample.column,
  sample.name = NULL,
  gene.column = NULL,
  deletion = "deletion",
  duplication = "duplication",
  ignore.unexpected.rows = FALSE,
  sep = "\t",
  skip = 0,
  genome = "hg19",
  exclude.non.canonical.chrs = TRUE,
  check.names.cnvs.file = FALSE
)

Arguments

cnvs.file	Path to csv/tsv file containing the CNV calls.
chr.column	Which column stores the chr location of the CNV.
start.column	Which column stores the start location of the CNV.
end.column	Which column stores the end location of the CNV.
coord.column	CNV location in the chr:start-end format. Example: "1:538001-540000". If NULL, chr.column, start.column and end.column columns will be used. (Defaults to NULL)
cnv.column	Which column stores the type of CNV (deletion or duplication).
sample.column	Which column stores the sample name.
sample.name	Sample name for all CNVs defined in cnvs.file. If set, sample.column is ignored (Defaults to NULL)
gene.column	Which columns store the gene or genes affected (optional). (Defaults to NULL)
deletion	Text used in the cnv.column to represent deletion CNVs. Multiple values are also allowed, for example: c("CN0", "CN1"). (Defaults to "deletion")
duplication	Text used in the cnv.column to represent duplication CNVs. Multiple values are also allowed, for example: c("CN3", "CN4") (Defaults to "duplication")
ignore.unexpected.rows	Whether to ignore the rows which CNV cnv.column value is different to deletion or duplication values (Defaults to FALSE). It is useful for processing output from callers like LUMPY or Manta (they call also events that are not CNVs)
sep	Separator symbol to load the csv/tsv file. (Defaults to "\t")
skip	Number of rows that should be skipped when reading the csv/tsv file. (Defaults to 0)
genome	The name of the genome. (Defaults to "hg19")
exclude.non.canonical.chrs	Whether to exclude non canonical chromosomes (Defaults to TRUE)
check.names.cnvs.file	Whether to check cnvs.file names or not (Defaults to FALSE). If TRUE then column names in the cnvs.file are checked to ensure that they are syntactically valid variable names. If necessary they are adjusted (by make.names) so that they are, and also to ensure that there are no duplicates

Details

Loads a csv/tsv file containing CNV calls, and transform it into a GRanges with cnv and sample metadata columns.

Value

A GRanges with a range per each CNV and the metadata columns:

• cnv: type of CNV, "duplication" or "deletion"

• sample: sample name

Returns NULL if cnvs.file has no CNVs

Examples

# Load CNVs data
cnvs.file <- system.file("extdata", "DECoN.CNVcalls.csv", package = "CNVfilteR", mustWork = TRUE)
cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample")

CNVfilteR documentation built on April 17, 2021, 6:06 p.m.