Description Usage Arguments Value Examples
nbor_order sorts individual cells according to their various stages during transition to resemble the landmark-to-landmark continuum
1 2 | nbor_order(exprs, ccFile, lm_order = c("CD115+CDP_1", "PreDC_9", "PreDC_10",
"PreDC_11"), if_bb_only = FALSE, method = 1, writeRes = TRUE)
|
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 |
a vector of re-orderd cell IDs
1 2 3 4 5 6 7 8 9 10 | ## 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)
|
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