set up the QC notebook with the data sets which are used throughout — sex_mislabel_setup • llfsRnaseq

set up the QC notebook with the data sets which are used throughout

sex_mislabel_setup(
  dds_rds_path,
  percent_samples_for_expr_fltr = 0.015,
  cpm_count_thres = 3
)

Arguments

dds_rds_path: path to a dds object, either gene or transcript counts
percent_samples_for_expr_fltr: this is used to set a minimum number of samples which have more than a certain number of cpm count. ie num_samples = floor(ncol(dds)*percent_samples_for_expr_fltr)
cpm_count_thres: the number of cpm required for a given gene to pass in a given sample. ie expr_fltr = rowSums(cpm(counts(dds)) > cpm_count_thres ) >= num_samples

Value

a list which contains the raw, expression filtered and expression filtered and passing sets