OmicSelector_counts_to_log10tpm: OmicSelector_counts_to_log10tpm

In kstawiski/OmicSelector: OmicSelector - a package for biomarker selection based on high-throughput experiments.

OmicSelector_counts_to_log10tpm

Description

Counts to log-transformed TPM-normalized counts. The funcction support additional filter, i.e. it can leave miRNAs that appear in minimum of 'filtr_minimalcounts' counts in 'filtr_howmany' samples. Usage of the filter like that can assure that the miRNAs selected will be detectable in qPCR.

Usage

OmicSelector_counts_to_log10tpm(
  danex,
  metadane = metadane,
  ids = metadane$ID,
  filtr = T,
  filtr_minimalcounts = 10,
  filtr_howmany = 1/2,
  increment = 0.001
)

Arguments

danex	Matrix with miRNA counts with miRNAs in columns and cases in rows.
metadane	Metadata with 'Class' variable.
ids	Unique identifier of samples.
filtr	If expression filter should be used.
filtr_minimalcounts	How many counts?
filtr_howmany	In how many samples? (Please provide a percentage or proportion, e.g. 1/2 or 1/3).
increment	Increment added to TPM values before log-transformation (usually: 0.001, so -3 will be equalt to lack of expression).

Value

Normalized counts in 'ttpm' format. Please note, that the function also saves 'TPM_DGEList_filtered.rds' to working directory, which is a DGEList object that can be used in packages like edgeR.

kstawiski/OmicSelector documentation built on April 10, 2024, 11:11 p.m.