gset(
S,
N = NULL,
r = NULL,
p = 1,
min_its = 200,
max_its = 1e+05,
significance_threshold = 0.05,
log_dismiss = -10,
raw_score = FALSE
)
Value
Numeric value - p-value of enrichment.
Arguments
S
Ranks of gene set
N
Integer value. Only required if r is not specified.
r
Rank/correlation scores. If S is character, then r must be named by gene or be a character vector of the gene names in rank order (necessarily containing S).
p
Weighting of ranking/correlations, see Subramanian et. al 2005.
min_its
Minimum number of null permutations to compare.
max_its
Maximum number of null permutations to compare.
significance_threshold
Maximum p-value of significant result.
log_dismiss
Threshold log probability of returning a significant result, below which function returns current p-value.
raw_score
Logical value determining whether to return the raw value of the gene set enrichment score.