filter_Tx: Filter out undesired transcripts from gencode gff files

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

Description

filter_Tx returns a filtered TxDb object

Usage

filter_Tx(gff, filter = TRUE, protein.coding = FALSE)

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.
filter	A logical scalar. Should transcripts with undefined ends and support levels higher than 2 (low confidence transcripts) be removed? The default is to remove low confidence transcripts (filter == TRUE)
protein.coding	A logical scalar. Should all transcripts that lack a protein coding tag be removed? The default is to keep all transcripts regardless of protein coding status (protein.coding == FALSE)

Value

The output from filter_Tx() is a TxDb object containing a gene model of the filtered transcripts This Txdb object is required for downstream functions. See https://www.rdocumentation.org/packages/GenomicFeatures/versions/1.24.4/topics/TxDb-class for more information

Examples

# No filtering
hs_TxDb <- filter_Tx(system.file("extdata", "gencode.v33.annotation.gff3.gz", package = "FeatureReachR"), filter = FALSE, protein.coding = FALSE)
mm_TxDb <- filter_Tx(system.file("extdata", "gencode.vM20.annotation.gff3.gz", package = "FeatureReachR"), filter = FALSE, protein.coding = FALSE)

# Filter out low confidence transcripts
hs_filtered_TxDb <- filter_Tx(system.file("extdata", "gencode.v33.annotation.gff3.gz", package = "FeatureReachR"))
mm_filtered_TxDb <- filter_Tx(system.file("extdata", "gencode.vM20.annotation.gff3.gz", package = "FeatureReachR"))

# Filter out low confidence transcripts and non-coding transcripts
hs_coding_TxDb <- filter_Tx(system.file("extdata", "gencode.v33.annotation.gff3.gz", package = "FeatureReachR"), protein.coding = TRUE)
mm_coding_TxDb <- filter_Tx(system.file("extdata", "gencode.vM20.annotation.gff3.gz", package = "FeatureReachR"), protein.coding = TRUE)

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