ap_reactsummary2: Calculate reactivity frequencies

In cekehe/rappp: QC, data transformation and visualization for PAPP

Calculate reactivity frequencies

Description

Calculate number of reactivities and the corresponding frequencies in Autoimmunity Profiling data.

Usage

ap_reactsummary2(x, samplegroups = NULL, percdec = 1, check.names = FALSE)

Arguments

x	List with at least two elements, see Details for naming and content.
samplegroups	factor vector of groupings. Only samples with an assigned level are included in plots. If left as NULL (default), the all non-filtered, if filetring done otherwise all, will be assigned "Sample".
percdec	integer indicating the number of decimal places in percentage value.
check.names	logical, altered default from data.frame().

Details

The x list needs to include at least the elements:

SAMPLES = Sample info, if any should be excluded then these should be annotated in a column called "Filtered". Any samples with no text (ie. "") in such column will be included. Column "sample_name" with sample names needed.

BINARY = list with one data.frame per cutoff

Optional element:

BINARY_CO = Binary table based on antigen specific cutoffs from ap_cutoff_selection2().

Value

A list with the elements

SAMPLEGROUPS = annnotation of which group each sample has been assigned,

REACTSUM_AG = number of reactive samples per antigen and sample group,

REACTFREQ_AG = reactivity frequency per antigen and sample group,

REACTSUM_SAMP = number of reactive antigens per sample,

REACTFREQ_SAMP = reactivity frequency per sample,

cekehe/rappp documentation built on May 17, 2022, 8:54 a.m.