a_sample_gene_set_rank_test: Perform a rank-based single sample gene set analysis.
In dolchan/ssgsrt: Single sample gene set rank test

Description Usage Arguments Value Examples

This function performs a rank-based single sample gene set analysis for a sample (x) and a list of gene sets (geneset_list).

1 2	a_sample_gene_set_rank_test(x, geneset_list, row_names = NULL, alternative = "two.sided", test.method = "ks")

`x`	a sample in a named array format.
`geneset_list`	a named list of gene sets, each of list element is named and a list ofgenes.
`row_names`	a list of (gene) names of x. Useful when names(x) is NULL.
`alternative`	`c('less','greater','two.sided')`. If 'less'/'greater', test if the overall gene expression of given gene set is lower/higher than the rest. If 'two.sided', test either lower or higher. Defaults to 'two.sided'.
`test.method`	`c('ks.test', 'wilcox.test')`. Defaults to 'ks'.

a list of z.stat, D (ks.test) or W (wilcox.test) stat, p.value, and adj.p.value (FDR) for each gene set. z.stat indicates if the gene set expression is "lower" (negative) or "higher" (positive). We use p-value estimated from the actual statistical test (ks.test or wilcox.test) and use normal distribution to compute "pseudo" z statistics.