add_scaled_counts_bulk.calcNormFactor {tidybulk} | R Documentation |
Calculate the norm factor with calcNormFactor from limma
add_scaled_counts_bulk.calcNormFactor( .data, reference = NULL, factor_of_interest = NULL, minimum_counts = 10, minimum_proportion = 0.7, .sample = sample, .transcript = transcript, .abundance = count, method )
.data |
A tibble |
reference |
A reference matrix, not sure if used anymore |
factor_of_interest |
The name of the column of the factor of interest |
minimum_counts |
A positive integer. Minimum counts required for at least some samples. |
minimum_proportion |
A real positive number between 0 and 1. It is the threshold of proportion of samples for each transcripts/genes that have to be characterised by a cmp bigger than the threshold to be included for scaling procedure. |
.sample |
The name of the sample column |
.transcript |
The name of the transcript/gene column |
.abundance |
The name of the transcript/gene abundance column |
method |
A string character. The scaling method passed to the backend function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile") |
A list including the filtered data frame and the normalization factors