SnapATAC (version 1.0.0)

runDimReduct: Linear Dimentionality Reduction

Description

This function takes a snap obj as input and performs computation of linear dimentionality reduction method using irlba

Usage

runDimReduct(obj, pc.num, input.mat, method, center, scale, seed.use, maxit,
  ...)

Arguments

obj

A snap obj.

pc.num

An integer number of dimetions to return [50].

input.mat

A character value indicates what input matrix to use - could be c("nmat", "jmat", "bmat", "pmat") [nmat].

method

A character value indicates what linear dimentionality reduction method to use - could be c("svd", "pca.whiten", "pca") [svd].

center

A logical value indicating whether the variables should be centered to be zero [TRUE].

scale

A logical value indicating whether the variables should be scaled to be standarized [FALSE].

seed.use

A numeric integer value interpreted as an integer [10].

maxit

Maximum number of iterations [1000].

...

Arguments passed to irlba fuction.

Examples

# NOT RUN {
data(demo.sp);
demo.sp = runDimReduct(obj=demo.sp, pc.num=10, input.mat="jmat");

# }