selectNegSamples: selecting negative samples for training RafSee

In cma2015/RAP: Rank aggregation-based data fusion for gene prioritization

Description

Negative samples are selected based on their connectivity with positive samples in protein-protein interaction network. Of note, the user can also have a try to randomly selected negative samples with a given number.

Usage

  selectNegSamples(positives, PPIMat = NULL, balanced = TRUE,
                   ratio = 1, GenomeGeneID)

Arguments

positives	A vector of positive samples.
PPIMat	A matrix of PPI, which contains 3 coloums represent protein1, protein2, score respectively;Of note, negative samples will be selected randomly if this parameter is not assigned.
balanced	A logical value, where TRUE represents balance the positive and negative samples according to the ratio.
ratio	A numuric value of the the ratio between negative and positive samples.
GenomeGeneID	A vector of genome ID.

Value

A vector of selected negative samples

Author(s)

Jingjing Zhai, Chuang Ma

Examples

  ## Not run: 
    positives <- c("AT1G01060", "AT1G09530", "AT1G09570", "AT1G12610")
    GenomeID <- c("AT1G01060", "AT1G09530", "AT1G09570", "AT1G12610", "AT1G77300", "AT1G79730")
    negatives <- selectNegSamples(positives = positives, PPIMat = PPIMat, GenomeID = GenomeID)
  
## End(Not run)

cma2015/RAP documentation built on Aug. 18, 2019, 8:02 p.m.