uSORT_preProcess {uSORT} | R Documentation |
A data loading and pre-processing function which firstly identifies outlier cells and scarcely expressed genes.
uSORT_preProcess(exprs_file, log_transform = TRUE, remove_outliers = TRUE, lod = 1)
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. |
A list containing exprs_raw
(data frame) and exprs_log_trimed
(data.frame).
dir <- system.file('extdata', package='uSORT') file <- list.files(dir, pattern='.txt$', full=TRUE) exprs <- uSORT_preProcess(exprs_file = file)