iProFun.detection: iProFun detection using multiple criteria

In songxiaoyu/iProFun: An integrative analysis tool to screen for Proteogenomic Functional traits perturbed by DNA alterations

iProFun detection using multiple criteria

Description

iProFun detection using multiple criteria

Usage

iProFun.detection(
  reg.all,
  eFDR.all,
  FWER.all = NULL,
  filter = c(0, 0),
  NoProbButFWERIndex = NULL,
  fdr.cutoff = 0.1,
  fwer.cutoff = 0.1,
  PostPob.cutoff = 0.75,
  xType,
  yType
)

Arguments

reg.all	reg.all is the regression results for all outcomes from 'iProFun.reg'.
eFDR.all	eFDR.all is eFDR results for all outcomes from 'iProFun.eFDR'.
FWER.all	FWER.all is FWER results for all outceoms from 'iProFun.FWER'. Can be NULL if FWER analysis was not performed.
filter	filter is a vector with the same length of xList, taking values of 1, -1, 0 or NULL. "NULL" is default imposes no filtering. 1" indicates that an association is considered for significance only if its significant associations are positive across all outcome platforms. "-1" indicates that an association is considered for significance only if its significant associations are negative across all outcome platforms. "0" indicates that an association is considered for significance only if its significant association across all outcome platforms preserve consistent directions (either positive or negative).
NoProbButFWERIndex	NoProbXIndex allows users to provide the index for the predictor data type(s) that are not considered for calculating posterior probabilities of association patterns. Default=NULL. All predictors go throught posterior probability calculation.
fdr.cutoff	Nominal false discover rate, default at 0.1
fwer.cutoff	family wise error rate cutoff to be considered as significant, default at 0.1.
PostPob.cutoff	Minimal posterior probability cutoff to be considered as significant, default at 0.75.
xType	A vector of string for the data types of xList, such as "mutation", "CNV" and "methylation", for output presentation.
yType	A vector of string for the data types of xList, such as "RNA", "protein" and "phospho", for output presentation.

Value

A output table that includes gene ID, other gene info if provided, predictor data type, outcome data type, estimate, se, p-value from Student's t-test, FWER, Posterior Association Probability, eFDR, directional filtering, and whether it's identified in iProFun or not, in a long format.

songxiaoyu/iProFun documentation built on Dec. 8, 2022, 3:54 p.m.