A data loading and pre-processing function

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Description

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

Usage

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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

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

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