filter_genes: Filter lowly abundant genes.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/filter_Genes.R

Description

filter_genes filters genes, according to the overall number of counts (across all samples) compatible with the gene. The filtering also applies to groups of genes with reads/fragments compatible with >1 gene; in this case, the number of counts considered is across all genes in the group.

Usage

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filter_genes(BANDITS_data, min_counts_per_gene = 10)

Arguments

BANDITS_data

a 'BANDITS_data' object, created with the create_data function.

min_counts_per_gene

the minimum number of counts compatible with a gene (across all samples).

Details

The function inputs a 'BANDITS_data' object, and returns again a 'BANDITS_data' object after filtering genes and groups of genes.

Value

A BANDITS_data object.

Author(s)

Simone Tiberi simone.tiberi@uzh.ch

See Also

filter_transcripts, create_data, BANDITS_data

Examples

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# load the pre-computed data:
data("input_data", package = "BANDITS")
input_data

# Filter lowly abundant genes:
input_data = filter_genes(input_data, min_counts_per_gene = 20)

SimoneTiberi/BANDITS documentation built on Aug. 7, 2020, 10:17 p.m.