Running SCnorm normalization

This function is a wrapper for SCnorm: robust normalization of single-cell RNA-seq data (Bacher et al. Nature Methods 2017, 14:584–586)

umiNorm(
  group = c("sudo", "docker"),
  file,
  outputName,
  normMethod = c("CLR_FN", "DESEQ_FN", "FQ_FN", "SCRAN_FN", "SUM_FN", "TMM_FN",
    "UQ_FN")
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

file,

a character string indicating the path of the file. IMPORTANT: full path to the file MUST be included. Only tab delimited files are supported

outputName,

specify the path and/or name of output files.

normMethod,

a string identifying the normalization method: CLR_FN, DESEQ_FN, FQ_FN, SCRAN_FN, SUM_FN, TMM_FN, UQ_FN, more info on the vignette.

Value

a tab delimited file containing the normalized data.

Examples

if (FALSE) {
    #downloading fastq files
    system("wget http://130.192.119.59/public/example_UMI.txt.zip")
    unzip("example_UMI.txt.zip")
    umiNorm(group="docker", file=paste(getwd(), "example_UMI.txt", sep="/"),
    outputName="example_UMI", normMethod="TMM_FN")
}