refNet: Create reference gene association network

In NabilaRahman/batchPred: batchPred - Objective prediction of relevant set of batch effects variables

Create reference gene association network

Description

refNet creates reference gene association network for batch effect evaluation. The output is required for create_ref_sample and batchPred functions.

Usage

refNet(
  network_gold_standard = NULL,
  input_edata = input_edata,
  gold_standard_path = NULL,
  false_positive = 0.025,
  true_positive = 0.5
)

Arguments

network_gold_standard	Datatable of gene-gene network gold standard. Column 1 and 2 are gene IDs. Column 3 is posterior probability with known edges set to 1. refNet is optimised for "full networks", which can be be downloaded from http://giant.princeton.edu/download/.
input_edata	Character vector of gene ids that exist within your expression dataset.
gold_standard_path	(Optional). Path to gene-gene network gold standard file. Can be specified in place of network_gold_standard.
false_positive	cutoff value for false positive gene-gene interactions. Only false positives with lower post probability are listed.
true_positive	cutoff value for true positive gene-gene interactions. Only true positives with higher post probability are listed.

Value

A reference gene association network for genes present in input_edata. This gold standard only retains the highest and lowest confidence gene interactions.Output is a data.table with columns 1 and 2 being gene ID, column 2 is posterior probability. While column 3 is defines whether gene relation is a true positive or false positive (0) based on user defined thresholds.

Examples

#Create Mock input gold standard
network_gold_standard<- data.table(
    V1 = c(3091,4763,4204,10628,4321,6359,5630,5630,100131077) 
    , V2 = c(7352,8698,6855,2475,5155,23513,100131077,751816,751816)
    , V3 =  c(1,1,1,1,1,1,0.0384244,0.00357639,0.0097727)
    , V4 = c(0.0193132,0.0299962,0.0244092,0.0437484,0.107417,0.0145827,NA
      ,NA,NA)
    , stringsAsFactors = F )
    
#Create Mock Gene IDs    
input_edata <- c('3091','4763','4204','7352','8698','6855' )

#Generate Reference Network
refNet( network_gold_standard, input_edata, 
gold_standard_path = NULL, false_positive = 0.025, true_positive = 0.5) 

NabilaRahman/batchPred documentation built on June 19, 2022, 5:35 a.m.