eff_len_compute {BANDITS} | R Documentation

## 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 simone.tiberi@uzh.ch

### 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)

[Package BANDITS version 1.2.3 Index]