DAFS: Calculates the threshold for a gene to be considered truly...

In KarenGoncalves/CustomSelection: Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis

Calculates the threshold for a gene to be considered truly expressed

Description

This function calculates the threshold for a gene to be considered truly expressed in each sample (columns of the expression data frame).

Usage

DAFS(tpm)

Arguments

tpm	Data frame of log2 transformed expression values (RPKM, FPKM, TPM, CPM, etc.). We recomend the use of the fuction Counts_to_tpm from this package. As the Counts_to_tpm function returns a list, use as input for DAFS the first object of its result, e.g.: DAFS(Counts_to_tpm(...)[[1]])

Details

Modified from George and Chang (2014).

The function normally requires two inputs: data and name. We do not export the result, so we do not need a 'name' argument.

Value

A vector with threshold for noise/true expression for each sample (columns from tpm data frame) in log2

Author(s)

George and Chang (2014)

References

doi:10.1186/1471-2105-15-92

Examples

data("sample_counts"); data("ath_featureLength")
tpm = Counts_to_tpm(counts = sample_counts, featureLength = ath_featureLength)
DAFS(tpm[[1]])

KarenGoncalves/CustomSelection documentation built on Oct. 24, 2023, 12:39 a.m.