loadCNVcalls {CNVfilteR} | R Documentation |
Loads CNV calls from a csv/tsv file
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 )
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, |
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 |
gene.column |
Which columns store the gene or genes affected (optional). (Defaults to NULL) |
deletion |
Text used in the |
duplication |
Text used in the |
ignore.unexpected.rows |
Whether to ignore the rows which CNV |
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 |
Loads a csv/tsv file containing CNV calls, and transform it into a GRanges with cnv
and sample
metadata columns.
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
# 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")