make_length_df: Create transcript length reference dataframe

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

Description

Because creating these dataframes takes a minute or two and its likely a user will be interested in multiple seq types (whole transcript, CDS, 5'UTR, 3'UTR) it is better to create and save this dataframe once.

Usage

make_longest_df(TxDb_gff)

make_median_df(TxDb_gff)

Arguments

TxDb_gff

A TxDb object. Using filter_Tx to create this TxDb object is recommended.

Value

Both make_longest_df and make_median_df create a dataframe relating Ensembl gene IDs and ensembl Transcript IDs. Because the longest CDS and longest 3'UTR for a gene may not belong to the same transcript, there is a column for each sequence type.

Functions

• make_longest_df: creates a dataframe of the transcripts with the longest features for each gene in a TxDb object

• make_median_df: creates a dataframe of the transcripts with the median length features for each gene in a TxDb object

See Also

filter_Tx, gene2tx

Examples

hs_filtered_TxDb <- filter_Tx("mydata/Gencodedat/gencode.v33.annotation.gff3.gz")
longest_hs <- make_longest_df(hs_filtered_TxDb)
median_hs <- make_median_df(hs_filtered_TxDb)

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