getDiffGenes | R Documentation |
given the lineage dependent expression profiles extracted by the getProfiles function, this function first smoothes the expression profile of each gene using cubic regression splines, fits to two models (M1: changes in the lineage; M0: no change), and then uses likelihood ratio test to compare the goodness of fit of the two models and assigns a p-value to each gene
getDiffGenes(
profiles,
diff.thresh = 0.1,
log.base = 2,
thresh.exp = 1,
thresh.cell = 2,
thresh.var = 0.5
)
profiles |
The lineage dependent gene expression profiles |
diff.thresh |
The FDR threshold for significance |
thresh.exp |
The expression threshold |
thresh.cell |
The cell number threshold |
thresh.var |
The variance threshold |
Genes meet the following criteria will be selected for likelihood ratio test: expression >=thresh.exp in at least thresh.cell cells and variance>=thresh.var Genes with FDR<diff.thresh will be considered significant
lineage dependent differentially expressed genes and their associated information, e.g., variance, pvalue, fdr, and M1 predicted expression
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