get_scaled_counts_bulk {tidybulk} | R Documentation |
Get a tibble with scaled counts using TMM
get_scaled_counts_bulk( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, factor_of_interest = NULL, minimum_counts = 10, minimum_proportion = 0.7, method = "TMM", reference_selection_function = median )
.data |
A tibble |
.sample |
The name of the sample column |
.transcript |
The name of the transcript/gene column |
.abundance |
The name of the transcript/gene abundance column |
factor_of_interest |
The name of the column of the factor of interest. This is used for identifying lowly abundant transcript, to be ignored for calculating scaling fators. |
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. |
method |
A character string. The scaling method passed to the backend function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile") |
reference_selection_function |
A function between median, mean and max |
A tibble including additional columns