sigminer (version 2.3.1)

transform_seg_table: Transform Copy Number Table

Description

Transform Copy Number Table

Usage

transform_seg_table(
  data,
  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
  ref_type = c("cytoband", "gene"),
  values_fill = NA,
  values_fn = function(x, ...) {
     round(mean(x, ...))
 },
  resolution_factor = 1L
)

Value

a data.table.

Arguments

data

a CopyNumber object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.

genome_build

genome build version, used when data is a data.frame, should be 'hg19' or 'hg38'.

ref_type

annotation data type used for constructing matrix.

values_fill

Optionally, a (scalar) value that specifies what each value should be filled in with when missing.

This can be a named list if you want to apply different fill values to different value columns.

values_fn

Optionally, a function applied to the value in each cell in the output. You will typically use this when the combination of id_cols and names_from columns does not uniquely identify an observation.

This can be a named list if you want to apply different aggregations to different values_from columns.

resolution_factor

an integer to control the resolution. When it is 1 (default), compute frequency in each cytoband. When it is 2, use compute frequency in each half cytoband.

Examples

# \donttest{
load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))
# Compute the mean segVal in each cytoband
x <- transform_seg_table(cn, resolution_factor = 1)
x
# Compute the mean segVal in each half-cytoband
x2 <- transform_seg_table(cn, resolution_factor = 2)
x2
# }