Transform Copy Number Table
transform_seg_table( data, genome_build = c("hg19", "hg38", "mm10", "mm9"), ref_type = c("cytoband", "gene"), values_fill = NA, values_fn = function(x, ...) { round(mean(x, ...)) }, resolution_factor = 1L )
data | a |
---|---|
genome_build | genome build version, used when |
ref_type | annotation data type used for constructing matrix. |
values_fill | Optionally, a (scalar) value that specifies what each
This can be a named list if you want to apply different aggregations to different value columns. |
values_fn | Optionally, a function applied to the This can be a named list if you want to apply different aggregations to different value columns. |
resolution_factor | an integer to control the resolution.
When it is |
a data.table
.
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