nbor_order: nbor_order sorts individual cells according to their various...

In Zouter/MPath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

nbor_order sorts individual cells according to their various stages during transition to resemble the landmark-to-landmark continuum

Usage

nbor_order(exprs, ccFile, lm_order = c("CD115+CDP_1", "PreDC_9", "PreDC_10",
  "PreDC_11"), if_bb_only = FALSE, method = 1, writeRes = TRUE)

Arguments

exprs	a data frame or matrix of expression data(ie. rpkm, TPM, fpkm) or a tab delimited txt file of expression data, containing cells in columns and genes in rows
ccFile	a data frame or matrix of two columns or a tab delimited file of landmark cluster assignment of individual cells. The first column indicates cell ID, the second column indicates the landmark cluster which the cell was assigned to.
lm_order	a vector of landmark IDs indicating along which path the cells are to be sorted
if_bb_only	a boolean to indicate if only cells on backbone will be sorted. Default is FALSE
method	1 or 2 to indicate which method to be used for sorting. Default is 1
writeRes	a boolean to indicate whether to save result files

Value

a vector of re-orderd cell IDs

Examples

## Not run: 
exprs = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG.txt";
ccFile = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG_landmark_cluster.txt";
order <- nbor_order(exprs = exprs,
                    ccFile = ccFile, 
                    lm_order = c("CDP_2","CDP_1","preDC_9","preDC_3"),
                    if_bb_only=FALSE,
                    method=1)

## End(Not run)

Zouter/MPath documentation built on May 4, 2019, 2:31 p.m.