GSARboot_format: Assemble GSNACA results on original dataset and bootstrap...

In hui-sheen/MetaGSCA: Meta-analysis of Gene Set differential Co-expression Analysis

Assemble GSNACA results on original dataset and bootstrap datasets

Description

Collate statistics and p-value of GSNCA on original dataset and counterpart statistics or median and CIs from bootstrap datasets

Usage

GSARboot_format(
  D_obs,
  pvalue,
  D_obs_boot,
  pvalue_boot,
  genes.not.found = "-",
  genes.removed = "-",
  nperm = 100,
  R = 200,
  level = 0.05,
  call = "Command used"
)

Arguments

D_obs	distance statistics from original dataset, by GSNCA
pvalue	p-value from original dataset, by GSNCA
D_obs_boot	distance statistics from multiple bootstrap datasets
pvalue_boot	p-values from multiple bootstrap datasets
genes.not.found	string of excluded genes for absence in expression matrix
genes.removed	string of genes that were removed for STD disqualification
nperm	number of permutations passed on to GSNCA
R	number of bootstrapping
level	confidence interval of this level. Defaults to 0.05 (95 percent CI)
call	external ultimate command exertion statement for GSAR_boot(). A character string

Details

Only one gene set is considered in the current function

Value

list of multiple objects of statistics value, where component dsetRow consists of 14 elements to appear as a row in output file

hui-sheen/MetaGSCA documentation built on April 9, 2022, 7:24 p.m.