View source: R/multi_enrichFRY.R
multi_enrichFRY | R Documentation |
Enrichment analyzer using roast
with function fry
.
multi_enrichFRY(
object,
G,
annot,
sep.str = " /// ",
symbol.col = "symbol",
grp = NULL,
contrast.v = ncol(design),
design = NULL,
weights = NULL,
trend = FALSE,
block = NULL,
correlation = NULL,
adjust.method = c("BH", "none"),
min.nfeats = 3,
max.nfeats = 1000,
pvalueCutoff = 0.25,
qvalueCutoff = 1
)
object |
Matrix-like data object containing log-ratios or log-expression values, with rows corresponding to features (e.g. genes) and columns to samples. Must have row names that are non-duplicated and non-empty. |
G |
Gene set list as returned from |
annot |
annotation for the features that has a column of the same type as in gene set list |
sep.str |
strings that separates symbols if there are multiple symbols for a feature. |
symbol.col |
column name or index for the symbol column in |
grp |
Vector of sample groups. These must be valid variable names in R and the same length as
|
contrast.v |
Named vector of contrasts, passed to |
design |
Design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated. |
weights |
Non-negative observation weights. Can be a numeric matrix of individual weights of same size as the
|
trend |
Logical; should an intensity-trend be allowed for the prior variance? Default is that the prior variance is constant. |
block |
Vector specifying a blocking variable on the samples. Has length = |
correlation |
Inter-duplicate or inter-technical replicate correlation. Must be given if
|
adjust.method |
Method used to adjust the p-values for multiple testing. Options, |
min.nfeats |
Minimum number of features (e.g. genes) needed in a gene set for testing. |
max.nfeats |
Maximum number of features (e.g. genes) needed in a gene set for testing. |
pvalueCutoff |
Cutoff value of pvalue. |
qvalueCutoff |
Cutoff value of qvalue. |
A list of 3 compareClusterResult
instance for up-regulated, down-regulated, and mixed-regulated enriched gene sets.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.