IndGOterm: The main function of individPath

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

Description

The function is used to screen personalized dysregulation terms. this function support parallel computation . You need to set thread numbers to make sure how many threads do you need to use.

Usage

IndGOterm(
  stable.pair,
  term,
  patients,
  threads = 1L,
  gene.minimum = 1L,
  threshold = 0.05,
  term_gene_list,
  non_redun
)

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.
term	a matrix or data.frame contains the informations of the terms in the Gene Ontology database. Download from http://archive.geneontology.org/lite/2019-07-06/. By default the variables are 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.
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.
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.
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).
non_redun	a vector of termID used to the screening of the personalized dysregulation terms.

Value

a list contained two data.frame , individual dyregulated pathway with term ID and individual dyregulated pathway with term name

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=stable.pair,reverse.pair=reverse_pairs,threads = 1,gene.minimum = 2,term_gene_list = BPtermgene_list,patients = patients,threshold = 0.05)
nonredundance<-remove.redundance(stable.pair = stable.pair,reverse.pair = reverse_pairs,gene.minimum = 2,patients = patients,re_graph = bp_graph,holidyregpath = global_dysterm,term_gene_list = BPtermgene_list,threads = 1)
samples2<-runif(50,min = 0,max = 50);
patients2<-matrix(c(geneid,samples2),nrow = 10,byrow=F);
result<-IndGOterm(stable.pair = stable.pair,term = term,patients = patients2,threads = 1,gene.minimum = 2,threshold = 0.05,term_gene_list = BPtermgene_list,non_redun = nonredundance$`non-redundant terms`)

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