runGSEA | R Documentation |
Computes gene set enrichment based on the results of
runDeAnalysis()
. See details for more.
runGSEA(
object,
across,
methods_de = "wilcox",
max_adj_pval = 0.05,
min_lfc = 0,
n_highest_lfc = NULL,
n_lowest_pval = NULL,
gene_set_list = NULL,
gene_set_names = NULL,
test = c("hypergeometric", "kstest"),
background = nGenes(object),
absolute = FALSE,
power = 1,
pval = 1,
fdr = 1,
reduce = TRUE,
quiet = TRUE,
chr_to_fct = TRUE,
verbose = NULL
)
object |
A valid spata-object. |
across |
Character vector. All grouping variables of interest. |
methods_de |
Character vector. All differential expression methods of interest. |
max_adj_pval |
Numeric value. Sets the threshold for adjusted p-values. All genes with adjusted p-values above that threshold are ignored. |
min_lfc |
Numeric value. Sets the threshold for average log fold change. All genes with an average log fold change below that threshold are ignored. |
n_highest_lfc |
Numeric value. Affects the total number of genes that are kept. See details. |
n_lowest_pval |
Numeric value. Affects the total number of genes that are kept. See details. |
gene_set_list |
A named list of character vectors. Names of slots correspond to the
gene set names. The slot contains the genes of the gene sets.Holds priority over
|
gene_set_names |
Character vector of gene set names that are taken from the object's gene set data.frame. |
test |
Character value. One of any. all, identical, not_identical and
none. Specifies how input for |
background |
Size or character vector of background population genes |
absolute |
Takes max-min score rather than the max deviation from null (kstest only) |
power |
Exponent for weights (kstest only) |
pval |
Filter results to be less than pval cutoff |
fdr |
Filter results to be less than fdr cutoff |
reduce |
Logical value. If set to TRUE (the default) the return value
of |
quiet |
Use true to suppress logs and warnings |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
Computes gene set enrichment analysis using hypeR::hypeR()
.
It does so by iterating about all possible combinations of across
and
methods_de
. Combinations for which no DE-results are found are silently
skipped.
If gene sets are provided via gene_set_list
argument gene_set_names
is ignored. Else the latter determines the gene sets used which are then taken
from the spata-objects gene set data.frame.
An updated spata-object.
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