sjdWrapProjection: SJD Wrap for projection

In CHuanSite/SJD: Structured Joint Decomposition (SJD)

SJD Wrap for projection

Description

Wrapping up a new list of projection matrices with the list computed from the function of sjdWrap

Usage

sjdWrapProjection(
  data.list.template,
  data.list.projection,
  species.template,
  species.vec.projection,
  geneType.template,
  geneType.vec.projection
)

Arguments

data.list.template	input list of expression matrices from the output of the sjdWrap function
data.list.projection	input list of expression matrices needed to be matched with data.list.template
species.template	character of species type from the sjdWrap function
species.vec.projection	list of species of each matrix to be projected
geneType.template	character of gene/rowname type from the sjdWrap function
geneType.vec.projection	list of output gene/rowname type of each matrix to be projected

Value

A list of expression matrices (of different species) with only shared genes to be projected

Examples

## Load NeuroGenesis4 data into R
data(NeuroGenesis4)

## sjdWrap of the training data sets
SJDdataIN = sjdWrap(
data.list = NeuroGenesis4,
species.vector=c("human","human","human","mouse"),
geneType.vector=c("symbol","ensembl","symbol","symbol"),
geneType.out="symbol",
species.out="human")

## Sample from data, serving as the projection expression matrices
NeuroGenesis4.sample = NeuroGenesis4
NeuroGenesis4.sample[[1]] = NeuroGenesis4.sample[[1]][-5,]
rownames(NeuroGenesis4.sample[[1]])[5] = paste0(rownames(NeuroGenesis4.sample[[1]])[5], ".test")

NeuroGenesis4.sample[[2]] = NeuroGenesis4.sample[[2]][-10,]
rownames(NeuroGenesis4.sample[[2]])[10] = paste0(rownames(NeuroGenesis4.sample[[2]])[10], ".test")

NeuroGenesis4.sample[[3]] = NeuroGenesis4.sample[[3]][-15,]
rownames(NeuroGenesis4.sample[[3]])[15] = paste0(rownames(NeuroGenesis4.sample[[3]])[15], ".test")

NeuroGenesis4.sample[[4]] = NeuroGenesis4.sample[[4]][-20,]
rownames(NeuroGenesis4.sample[[4]])[20] = paste0(rownames(NeuroGenesis4.sample[[4]])[20], ".test")

SJDdataProjection = sjdWrapProjection(
SJDdataIN, NeuroGenesis4.sample, "human", c("human","human","human","mouse"),
"symbol", c("symbol","ensembl","symbol","symbol"))

CHuanSite/SJD documentation built on Nov. 29, 2024, 5:52 a.m.