sestats_to_df: Convert sestats to table summary

In jmw86069/jamses: Jam SummarizedExperiment Stats

Convert sestats to table summary

Description

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

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.

Value

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

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)
}

jmw86069/jamses documentation built on Nov. 4, 2024, 9:25 p.m.