eff_len_compute: Compute the median effective length of transcripts.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/eff_len_compute.R

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

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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 simone.tiberi@uzh.ch

See Also

filter_transcripts, create_data

Examples

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# 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 Aug. 7, 2020, 10:17 p.m.