intern.chromo: Internal function

Description Usage Arguments Value Examples

View source: R/internal_functions.R

Description

Communicates between cursus and omnibus by coordinating a chromosome-wide analysis.

Usage

1
2
3
intern.chromo(Y, Ystart, Yend, X, Xloc,
             window, offset, group, perm,
             nodes, phi, kind)

Arguments

Y

RNA-Seq data: numeric matrix with q rows (genes) and n columns (samples); or a SummarizedExperiment object

Ystart

start location of genes: numeric vector of length q

Yend

end location of genes: NULL or numeric vector of length q

X

genomic profile: numeric matrix with p rows (covariates) and n columns (samples)

Xloc

location covariates: numeric vector of length p

window

maximum distance: non-negative real number

offset

numeric vector of length n

group

confounding variable: factor of length n

perm

number of iterations: positive integer

nodes

number of cluster nodes for parallel computation

phi

dispersion parameters: vector of length q

kind

computation : number between 0 and 1

Value

The function returns a dataframe, with the p-value in the first column, and the test statistic in the second column.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
# simulate high-dimensional data
n <- 30
q <- 10
p <- 100
set.seed(1)
Y <- matrix(rnbinom(q*n,mu=10,
    size=1/0.25),nrow=q,ncol=n)
X <- matrix(rnorm(p*n),nrow=p,ncol=n)
Yloc <- seq(0,1,length.out=q)
Xloc <- seq(0,1,length.out=p)
window <- 1

# hypothesis testing
cursus(Y,Yloc,X,Xloc,window)

globalSeq documentation built on Nov. 8, 2020, 7:22 p.m.