RNA_breakdown: Summarize RNA types in transcript list

In TaliaferroLab/FeatureReachR: Extract Enriched Biological Features From RNA-seq Data

Description

RNA_breakdown counts RNA types present in a transcript list and can be used to better understand your case and control sets of transcripts. If you instead have sets of genes, we recommend using expression data to find expresed transcripts within your experiment. Alternatively, use gene2tx() to create transcript sets from either make_longest_df or make_median_df

Usage

RNA_breakdown(gff, tx_list)

Arguments

gff	A path. To the human or mouse gencode annotation gff file. The most current annotations can be downloaded from: https://www.gencodegenes.org/human/ or https://www.gencodegenes.org/mouse/ There are two filter options, a general filter and a protein coding filter.
tx_list	A character list. Must contain Ensembl transcript IDs and be compatible with the gff (the same species)

Value

RNA_breakdown creates a y table containing both the number of transcripts categorized within an RNA type (count) and the percent of the total set an RNA type represents (percent).

See Also

gene2tx(), make_longest_df, make_median_df

Examples

mm_tx <- c("ENSMUST00000159265.1", "ENSMUST00000027032.5", "ENSMUST00000130201.7", "ENSMUST00000157375.1")
RNA_breakdown("mydata/Gencodedat/gencode.vM20.annotation.gff3.gz", mm_tx)

TaliaferroLab/FeatureReachR documentation built on Aug. 15, 2021, 2:21 p.m.