ks.counts_to_log10tpm: ks.counts_to_log10tpm

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

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

ks.counts_to_log10tpm(
  danex,
  metadane = metadane,
  ids = metadane$ID,
  filtr = T,
  filtr_minimalcounts = 10,
  filtr_howmany = 1/2
)

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).

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/miRNAselector documentation built on Oct. 10, 2020, 9:03 a.m.