outlier_analysis: With the grouptablist generated by count_outliers - run...

In ruggleslab/blackSheepR: Outlier Analysis for pairwise differential comparison

With the grouptablist generated by count_outliers - run through and run a fisher exact test to get the p.value for the difference in outlier count for each feature in each of your comparisons

Description

With the grouptablist generated by count_outliers - run through and run a fisher exact test to get the p.value for the difference in outlier count for each feature in each of your comparisons

Usage

outlier_analysis(grouptablist, fraction_table = NULL,
    fraction_samples_cutoff = 0.3,
    write_out_tables = FALSE, outfilepath = tempdir())

Arguments

grouptablist	table generated by the count_outliers function. NOTE that the inputted grouptablist will be deciphered to determine its content. This means that user decides to input the outliertab or aggregate tab, and the output will analyze according to what positive and negative information is contained within the table
fraction_table	DEFAULT: NULL; Input a fraction table to filter to only include features that have x an outlier.
fraction_samples_cutoff	DEFAULT: 0.3; Input a fractional cut off for the of samples that need to have an outlier for feature to be considered. ex) 10 samples in ingroup - 3 need to have an outlier for feature to be considered significant
write_out_tables	DEFAULT: FALSE; utility in function to write out each of the analyses to a separate table to whereever <outfilepath> is specfied.
outfilepath	the full string path to where the file should output to, DEFAULT is a tempdir()

Value

the analysis table with p.value, fdr, and raw data per comparison

Examples

data("sample_phosphodata")
reftable_function_out <- make_outlier_table(sample_phosphodata[1:1000,])
outliertab <- reftable_function_out$outliertab

data("sample_annotationdata")
groupings <- comparison_groupings(sample_annotationdata)

count_outliers_out <- count_outliers(groupings, outliertab,
    aggregate_features = FALSE)
grouptablist <- count_outliers_out$grouptablist
fractiontab <- count_outliers_out$fractiontab

outlier_analysis_out <- outlier_analysis(grouptablist,
    fraction_table = fractiontab)

ruggleslab/blackSheepR documentation built on Feb. 27, 2023, 10:39 p.m.