monocle_wrapper: A wrapper function for Monocle sorting method

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

Description

A wrapper function for Monocle sorting method

Usage

monocle_wrapper(log2_exp, expression_data_raw, lod = 1)

Arguments

log2_exp	An log2 transformed expresssion matrix containing n-rows of cells and m-cols of genes.
expression_data_raw	A data frame containing raw expression values, with rownames of cells and colnames of genes.
lod	A value of limit of detection in the unit of TPM/CPM/RPKM.

Value

A data frame containing single column of ordered sample IDs.

Examples

set.seed(15)
da <- iris[sample(150, 150, replace = FALSE), ]
rownames(da) <- paste0('spl_',seq(1,nrow(da)))
d <- da[,1:4]
dl <- da[,5,drop=FALSE]
#res <- monocle_wrapper(log2_exp = d, expression_data_raw = d)
#dl <- dl[match(res,rownames(dl)),]
#annot <- data.frame(id = seq(1,length(res)), label=dl, stringsAsFactors = FALSE)
#ggplot(annot, aes(x=id, y=id, colour = label)) + geom_point() + theme_bw()

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