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Convert sestats to table summary

Source: R/jam_sestats.R
sestats_to_df.Rd

Convert sestats to table summary

Usage

sestats_to_df(
  sestats,
  style = c("text", "integer"),
  dimname_order = c(3, 2, 1),
  rename_contrasts = FALSE,
  ...
)

Arguments

sestats

list output from se_contrast_stats()

style

character string indicating what values to use:

  • "text": number of hits (number up, number down)

  • "integer": only the integer number of hits

rename_contrasts

logical indicating whether to rename contrasts using contrast2comp(). The main benefit is reduction in length of the string that describes each contrast.

...

additional arguments are passed to contrast2comp(), which is relevant when rename_contrasts=TRUE, relevant arguments include:

  • contrast_delim="-" to

  • contrast_factor_delim="_" to customize the delimiter between factors in the input group names, for example "Treatment1_Time1" uses "_".

  • comp_factor_delim=":" to customize the delimiter between factors

  • factor_order=NULL to customize the order of factor comparisons

Value

data.frame with a summary of statistical hits per contrast, assay_name, and threshold.

Details

Note: This function is intended to provide a simple data.frame summary with the number of hits for each contrast, signal, cutoff. It is still being tested, and updated for usability.

TODO: The order of dimnames(hit_array) should be user-customizable. The series of dimnames in each lapply should use this order.

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(), voom_jam()

Examples

if (FALSE) {
hitdf <- sestats_to_df(list(hit_array=hit_array));
hitdf_rowindex <- table(hitdf[[1]])[unique(hitdf[[1]])]
jamba::kable_coloring(
   hitdf[, -1, drop=FALSE],
   row.names=FALSE) %>%
   kableExtra::pack_rows(index=hitdf_rowindex)
}