spans_make_distribution: Creates the list of median p-values used to make the...

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Creates the list of median p-values used to make the background distribution used to compute the SPANS score in step 2.

Description

Creates the list of median p-values used to make the background distribution used to compute the SPANS score in step 2.

Usage

spans_make_distribution(
  omicsData,
  group_vector,
  norm_fn,
  sig_inds,
  nonsig_inds,
  select_n
)

Arguments

omicsData	an object of the class 'pepData' or 'proData' created by as.pepData or as.proData, respectively.
group_vector	A character vector from the group_DF attribute specifying the order of the samples. This order is the same as the order of the samples (columns) in e_data.
norm_fn	a character vector of normalization methods to choose from. Current options are 'mean', 'median', 'zscore', and 'mad'.
sig_inds	significant peptide indices (row indices) based on a Kruskal-Wallis test on the un-normalized data
nonsig_inds	non-significant peptide indices (row indices) based on a Kruskal-Wallis test on the un-normalized data
select_n	number of peptide by sample indices in the data to randomly select to determine normalization parameters

Value

a list with 2 elements. The median of highly significant p-values, and the median of nonsignificant p-values. These are obtained from a SINGLE Kruskal-Wallis test on data normalized by scale/location factors determined from a randomly selected subset of peptides and normalization method

pmartR/pmartR documentation built on March 4, 2024, 8:32 a.m.