filter_reference: Filter GFF Reference Files

In colbyford/cytosieve: In silico cytometric filtering of bulk sequencing data using transcriptional profiles.

Description

Filter out genes from a GFF file that are not expressed in a particular stage/cell type of interest. Works by filtering out lines with genes that match based on a reference set of gene names.

Usage

filter_reference(gff, genes_names = NULL, eliminate_matches = TRUE,
  verbose = TRUE)

Arguments

gff	gffObject. Object from the read_gff function.
genes_names	Vector of strings. List of gene IDs by which to filter.
eliminate_matches	Logical. Should the matches that are found be filtered out (TRUE) or should non-matched be filtered out (FALSE)? (Default: TRUE)
verbose	Logical. Should the process print out which read and gene it is currently searching? (Default: TRUE)

Examples

gff_filtered <- filter_reference(gff, gene_names = c("geneA", "geneB"))

colbyford/cytosieve documentation built on April 24, 2021, 8:24 p.m.