OmicSelector_counts_to_log10tpm — OmicSelector_counts_to

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.