tpm_normalisation: TPM calculator

In irilenia/baerhunter: Detection and Analysis of Expressed Intergenic Elements in Bacterial RNA-seq Data

TPM calculator

Description

This function uses feature count tables to calculate TPM values for each gene and sample.

Usage

tpm_normalisation(
  count_table,
  complete_ann,
  feature_type = c("putative_sRNA", "putative_UTR"),
  is_gff = T,
  output_file = NA,
  excl_rna = T
)

Arguments

count_table	A CSV file containing feature counts for each sample.
complete_ann	A GFF3 annotation file or SAF dataframe
feature_type	A string indicating desired feature type(s) from annotation.
is_gff	A boolean indicating whether annotation is gff file, default=T
output_file	A string indicating the name of the output file.
excl_rna	A boolean indicating if misc RNA features (rRNA, tRNA) are excluded from normalisation. (Defaults=T)

Value

A dataframe with TPM values for each gene and sample; the same is written into the output file.

irilenia/baerhunter documentation built on May 18, 2024, 11:56 p.m.