calculate RLE by replicate groups

calculate RLE by replicate groups

Usage

rleByReplicateGroup(replicates_vector, gene_quants, log2_transformed_flag)

Arguments

replicates_vector

a list of lists where each sublist represents a replicate group. Entries must be a metadata parameter, such as fastqFileName, that corresponds to the columns of the counts. Suggestion: use something like these dplyr functions to create the list of lists group_by() %>% group_split %>% pull(fastqFileName)

gene_quants

a gene x sample dataframe with values as some sort of gene quantification (eg normed counts, or log2(norm_counts) with some effect removed), possibly already logged (@see already_logged_flag)

log2_transformed_flag

a boolean where TRUE means the counts are already in log2 space

Value

a list of dataframes for each replicate group in replicateS_sample_list, each with dimensions gene x sample. values are RLE of the gene in a given sample

See also

rlePlotCompareEffectRemoved to plot the norm counts and removedEffect 'counts' on the same plot