eff_len_compute: Compute the median effective length of transcripts.

In SimoneTiberi/BANDITS: BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Compute the median effective length of transcripts.

Description

eff_len_compute inputs the estimated effective length of transcripts from every sample, and computes the median effective length of each transcript across samples.

Usage

eff_len_compute(x_eff_len)

Arguments

x_eff_len

is a list: each element of the list refers to a specific sample and is a matrix or data.frame with the estimated effective length under the column 'EffectiveLength' and the transcript name under the column 'Name'.

Value

A vector containing the effective length of transcripts; the vector names indicate the transcript ids.

Author(s)

Simone Tiberi [e-mail]

See Also

filter_transcripts, create_data

Examples

# specify the directory of the internal data:
data_dir = system.file("extdata", package = "BANDITS")

# Specify the directory of the transcript level estimated counts.
quant_files = file.path(data_dir, "STAR-salmon", paste0("sample", seq_len(4)), "quant.sf")

# Load the transcript level estimated counts via tximport:
library(tximport)
txi = tximport(files = quant_files, type = "salmon", txOut = TRUE)

# compute the Median estimated effective length for each transcript:
eff_len = eff_len_compute(x_eff_len = txi$length)
head(eff_len)

SimoneTiberi/BANDITS documentation built on Nov. 15, 2023, 2:35 p.m.