get.globdysterm: get holistic dyregulated pathway

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

Description

the function is used to get global dysregulation terms 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

get.globdysterm(
  stable.pair,
  reverse.pair,
  threads = 1L,
  gene.minimum = 1,
  term_gene_list = BPtermgene_list,
  patients,
  threshold = 0.05
)

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.
reverse.pair	a matrix or data.frame of reverse pairs from disease samples with two columns, the expression of the genes in the first column is higher than that in the second column.
threads	an integer value to make sure how many threads you will use to complete the computation.
gene.minimum	an integer value to control the minimum amount of the genes of the terms. The deault is 1.
term_gene_list	a list of term genes. list type. each list is a vector type, containing all the genes of a term. By default the variables are "BPtermgene_list" and taken from environment(formula).
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 exact probability test , default is 0.05.

Value

a data.frame containing three columns represent "termID" , "p value" , "fdr value" respectively

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)
global_dysterm<-get.globdysterm(stable.pair,reverse_pairs,threads = 1,gene.minimum = 2,term_gene_list = BPtermgene_list,patients = patients,threshold = 0.05)

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