reliableFeatures: Identify features (e.g., transcripts) with high quality data

In bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

Identify features (e.g., transcripts) with high quality data

Description

This function identifies all features (e.g., transcripts, exons, etc.) for which the mutation rate is below a set threshold in the control (-s4U) sample and which have more reads than a set threshold in all samples. If there is no -s4U sample, then only the read count cutoff is considered. Additional filtering options are only relevant if working with short RNA-seq read data. This includes filtering out features with extremely low empirical U-content (i.e., the average number of Us in sequencing reads from that feature) and those with very few reads having at least 3 Us in them.

Usage

reliableFeatures(
  obj,
  high_p = 0.2,
  totcut = 50,
  totcut_all = 10,
  Ucut = 0.25,
  AvgU = 4
)

Arguments

obj	Object of class bakRData
high_p	highest mutation rate accepted in control samples
totcut	Numeric; Any transcripts with less than this number of sequencing reads in any replicate of all experimental conditions are filtered out
totcut_all	Numeric; Any transcripts with less than this number of sequencing reads in any sample are filtered out
Ucut	Must have a fraction of reads with 2 or less Us less than this cutoff in all samples
AvgU	Must have an average number of Us greater than this

Value

vector of gene names that passed reliability filter

Examples

# Load cB
data("cB_small")

# Load metadf
data("metadf")

# Create bakRData
bakRData <- bakRData(cB_small, metadf)

# Find reliable features
features_to_keep <- reliableFeatures(obj = bakRData)

bakR documentation built on June 22, 2024, 6:55 p.m.