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Limma-voom customized for Jam

Source: R/jam_secontrasts.R
voom_jam.Rd

Limma-voom customized for Jam

Usage

voom_jam(
  counts,
  design = NULL,
  lib.size = NULL,
  normalize.method = "none",
  block = NULL,
  correlation = NULL,
  weights = NULL,
  span = 0.5,
  plot = FALSE,
  save.plot = TRUE,
  verbose = FALSE,
  ...
)

Details

This function is based directly upon limma::voom() with a small adjustment to handle the presence of NA values, which otherwise causes the stats::lowess() output to be clearly incorrect. The correction removes NA values during this step, producing a result as expected.

See also

Other jamses stats: ebayes2dfs(), format_hits(), handle_na_values(), hit_array_to_list(), process_sestats_to_hitim(), run_limma_replicate(), save_sestats(), se_contrast_stats(), sestats_to_dfs(), sestats_to_df()