get_gene_copy_numbers | R Documentation |
Takes a jabba_rds output and returns a GRanges with the genes that have either amplifications or deletions
get_gene_copy_numbers(
gg,
gene_ranges,
nseg = NULL,
gene_id_col = "gene_id",
simplify_seqnames = FALSE,
mfields = c("gene_name", "source", "gene_id", "gene_type", "level", "hgnc_id",
"havana_gene"),
output_type = "data.table"
)
gg |
either path to rds of a gGraph or an object containing the gGraph with JaBbA output |
gene_ranges |
GRanges of genes (must contain field "gene_name"). Alternatively a path to a file that could be parsed by rtracklayer::import (such as gtf) is acceptable. |
nseg |
GRanges with field "ncn" - the normal copy number (if not provided then ncn = 2 is used) |
gene_id_col |
the name of the column to be used in order to identify genes (must be unique for each gene, so usually "gene_name" is not the right choice). |
simplify_seqnames |
when set to TRUE, then gr.sub is ran on the seqnames of the gGraph segments and the genes GRanges |
mfields |
the metadata fields that the output should inherit from the genes GRanges |
output_type |
either GRanges or data.table |
GRanges or data.table with genes CN
Alon Shaiber
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