preprocessDat: Pre-process the data for SAVER-X

In jingshuw/SAVERX: Transfer Learning for Single-cell RNA-seq Denoising

Pre-process the data for SAVER-X

Description

Pre-process the data for SAVER-X

Usage

preprocessDat(out.dir, input.file.name = NULL, data.matrix = NULL,
  data.species = c("Human", "Mouse", "Others"),
  model.species = c("Human", "Mouse", "Joint"), model.nodes.ID = NULL)

Arguments

out.dir	a directory store all intemediate files. Can be generated automatically by this function is called by computePrediction
input.file.name	Can be either .txt, .csv or .rds files that store the data matrix gene by cell, or can be NULL is data.matrix is provided. The rds file can either store the data as a regular matrix or a sparse matrix
data.matrix	a matrix of UMI counts. Should be NULL if input.file.name is provided. The matrix is gene by cell with gene and cell names. Can be either a regular or sparse matrix.
data.species	The species of the dataset
model.species	The species of the pretrained model
model.nodes.ID	The vector of node IDs of the pretrained model (only needed for the species of the data when the pre-trained model is joint). Set to NULL if running SAVER-X without pretraining.

Value

Do not return anything but generate a series of intermediate files in the out.dir

jingshuw/SAVERX documentation built on June 20, 2022, 3:17 a.m.