format_hits: Format list of hit vectors into summary counts

In jmw86069/jamses: Jam SummarizedExperiment Stats

Format list of hit vectors into summary counts

Description

Format list of hit vectors into summary counts

Usage

format_hits(hits, style = c("text", "integer", "vector"), ...)

Arguments

hits	list, array, or vector with values c(-1, 1) indicating hits down, or hits up, respectively. When any vector contains only NA values, then NA is also returned. This distinction is as follows: NA values indicate the statistical contrast was not performed, which happens when se_contrast_stats() arguments for interaction contrasts differ from pairwise contrasts, for example int_adjp_cutoff, int_p_cutoff, or int_fold_cutoff. length==0 indicates the statistical contrast was performed, and there were no statistical hits for the given cutoffs.
style	character string indicating the output format: "text": character string with "hits(hits up, hits down)". "integer": integer number of hits, or NA when the test was not performed. "vector": integer vector with names ⁠("hit", "up", "down")⁠.
...	additional arguments are ignored.

Details

This function is used by sestats_to_df(), to summarize hits for each contrast into one of these formats:

• string summary of statistical hits with "hits,up,down" when style="text", for example: "623 hits (267 up, 379 down)"

• integer count of statistical hits when style="integer", for example: 623.

• vector of integer counts for c("hits", "up", "down"), for example: c(hits=623, up=267, down=379).

The function may be useful outside of sestats_to_df() so it is exported as a convenience function.

Value

the same data type as input, where the hit vector is replaced with a single value summarizing the hits. The data types have three expected options:

• array: when used with hit_array data from se_contrast_stats()

• list: when used on a particular subset of hit_array data

• numeric: when used with a single contrast

See Also

Other jamses stats: ebayes2dfs(), 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(), voom_jam()

Examples

set.seed(123)
hitlist <- list(
   `groupA-groupB`=sample(c(-1, 1), size=25, replace=TRUE),
   `groupA-groupC`=sample(c(-1, 1), size=50, replace=TRUE))
format_hits(hitlist, style="text")
format_hits(hitlist, style="integer")

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