votedEP: Returns voted EP pairs for the combination of cohort/method/...

In BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements

Description

This function allows easy import of results of different voting procedures for given combination of cohort/method/algorithm.

Usage

votedEP(indexTable, votingType = "votingAlgoritm", method = "H3K4me1",
  algorithm = "pearson", cohort = "Roadmap")

Arguments

indexTable	an output of the makeIndexTable() for given combination of methods/algorithms/cohorts; a table should contain the following columns: path - paths to .rds files; methods - a method type used for the analysis: eg. H3K4me1; algorithms - algorithm used for the analysis: eg. dcor, cohorts - cohort used for the analysis: eg. Roadmap; type - define whether results are produced by voting, meta-analysis, from individual modelling or a result of regActivityAroundTSS()
votingType	"votingAlgoritm" (default; character) Describes which voting procedure was used to produce voting results. OPTIONS: ("votingAlgoritm","votingCohorts","votingMethods").
method	"H3K4me1" (default; character). For which method to extract Enh~Promoter pairs. Common options: "H3K4me1","H3K27ac", "Methylation","DNase"
algorithm	"pearson" (default; character). For which algorithm to extract Enh~Promoter pairs. Common options:"pearson","spearman", "elasticnet","dcor","randomForest"
cohort	"Roadmap" (default; character). For which cohort to extract Enh~Promoter pairs. Common options:"Roadmap","Blueprint", "CEMT","McGill"

Details

This function allows easy import of results of different voting procedures for given combination of cohort/method/algorithm. For example, "votingAlgoritm" correspond to voting based on the results of pearson, spearman,elasticnet,dcor,randomForest modelling procedures for a combination of cohort and method (eg H3K4me1+Roadmap). In this case algorithm argument is ignored while importing "votingAlgoritm" results for H3K4me1+Roadmap

Author(s)

Inga Patarcic

Examples

## Not run: 
library(InteractionSet)
library(stringr)
IndexTable <- readRDS("/data/akalin/Projects/AAkalin_Catalog_RI/Results/Validation/Fishillevic/VoteD//CohortVoting_McGillH3K4me1.rds")

votedEP(indexTable,
votingType="votingAlgorithm",
method="H3K4me1",
algorithm="pearson",
cohort="Roadmap")
 

## End(Not run)

BIMSBbioinfo/reg2gene documentation built on May 3, 2019, 6:42 p.m.