revpairs: get reverse pairs from all the tumor samples

In robert19960424/IndGOterm: Tools for filtrating dysregulation terms from personalized patient

Description

the function is used to get reverse gene pairs from a host of disease samples. this function support parallel computation . You need to set thread numbers to make sure how many threads do you need to use .

Usage

revpairs(
  stable.pair,
  patients,
  threshold = 0.05,
  spairs_threshold = 0.99,
  threads = 1L,
  capacity = 300000L
)

Arguments

stable.pair	a matrix or data.frame of stable pairs from normal samples with two columns, the expression of the genes in the first column is higher than that in the second column.
patients	a matrix of data.frame of tumor samples , the first column must be the geneID ,and tumor samples start with the second column.
threshold	a numeric value which is used to control false discovery rate under the p_value of the chip-square test or fisher's exact probability test , default is 0.05.
spairs_threshold	a threshold same with the "threshold" in function "spairs".
threads	an integer value to make sure how many threads you will use to complete the computation
capacity	an integer value to depict the computation capacity, ruling how many lines of stable pairs would be computed within one time.the default is 300000

Value

a matrix containing four columns respectively represent higher expression gene , lower expression gene , p_value under binomial distribution , false discovery rate under p.adjust

Examples

stable.pair<-t(combn(sample(1:10,10),2));
geneid<-1:10;
samples<-runif(100,min = 0,max = 50);
patients<-matrix(c(geneid,samples),nrow = 10,byrow=F);
reverse_pairs<-revpairs(stable.pair,patients,threshold=0.05,spairs_threshold=0.99,threads=1L,capacity=300000L)
#compute with parallel
reverse_pairs<-revpairs(stable.pair,patients,threshold=0.05,spairs_threshold=0.99,threads=10L,capacity=300000L)

robert19960424/IndGOterm documentation built on Feb. 9, 2021, 8:37 a.m.