runDimReduct: Linear Dimentionality Reduction

In r3fang/SnapATAC: Single Nucleus Analysis Package for ATAC-Seq

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

data(demo.sp);
demo.sp = runDimReduct(obj=demo.sp, pc.num=10, input.mat="jmat");

r3fang/SnapATAC documentation built on March 29, 2022, 4:33 p.m.