uSORT_preProcess: A data loading and pre-processing function

In JinmiaoChenLab/uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description

A data loading and pre-processing function which firstly identifies outlier cells and scarcely expressed genes.

Usage

uSORT_preProcess(exprs_file, log_transform = TRUE, remove_outliers = TRUE,
  lod = 1)

Arguments

exprs_file	Input file name in txt format, with rownames of cells and colnames of genes.
log_transform	Boolean, if TRUE log transform the data.
remove_outliers	Boolean, if TRUE remove the outliers.
lod	A value of limit of detection in the unit of TPM/CPM/RPKM. It will be used as the starting value for outlier cell detection and the basis for removing scarce genes.

Value

A list containing exprs_raw(data frame) and exprs_log_trimed(data.frame).

Examples

dir <- system.file('extdata', package='uSORT')
file <- list.files(dir, pattern='.txt$', full=TRUE)
exprs <- uSORT_preProcess(exprs_file = file)

JinmiaoChenLab/uSORT documentation built on May 7, 2019, 10:53 a.m.