run_SCDE: Run single-cell differential expression testing on a...
In adamnc2/simpleSCDE: Simplified Cell Data Manipulation and SCDE Testing

Description Usage Arguments Value Examples

Run single-cell differential expression testing on a specified data frame of cells and genes

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run_SCDE(df, labels, write_to_txt = FALSE, file_name = "results.txt",
  ncores = 1, min_genes_detected = 1800, min_reads_per_gene = 10,
  min_cells_gene_in = 5)

`df`	A data frame
`labels`	A vector containing labels indicating if certain cells positively or negatively express personal genes
`write_to_txt`	Boolean indicating whether results should be written to an external text file (default: FALSE)
`file_name`	Full file name to use for document containing test results
`ncores`	Number of cores to utilize (default: 1)
`min_genes_detected`	Minimum number of genes detected in a cell. Cells with fewer genes will be removed (default: 1.8e3)
`min_reads_per_gene`	Minimum number of reads per gene. Genes with fewer reads will be removed (default: 10)
`min_cells_gene_in`	Minimum number of cells a gene must be seen in. Genes not seen in a sufficient number of cells will be removed (default: 5)

data frame containing upper bound(ub), maximum likelihood estimate(mle), upper bound(ub), conservative estimate(ce), Z-score(Z), and cZ-score(cZ) values

slit_posneg <- pos_neg.label(df = es.mef.small,
                             rowname = "dd_Smed.v4_12111_0_1")
run_SCDE(df = Fincher, labels = slit_posneg, file_name = "slitResults.txt",
         min_genes_detected = 10)