View source: R/limma_ftest_contrasts.R
limma_ftest_contrasts | R Documentation |
Apply limma's lmFit
, contrasts.fit
, & eBayes
to one or more contrasts, perform moderated F-test, and return
a table.
limma_ftest_contrasts(
object,
grp = NULL,
contrast.v,
add.means = !is.null(grp),
weights = NA,
design = NULL,
prefix = "",
trend = FALSE,
block = NULL,
correlation = NULL
)
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. |
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 |
add.means |
Logical indicating if (unweighted) group means per row should be added to the output. |
weights |
Non-negative observation weights. Can be a numeric matrix of individual weights of same size as the
|
design |
Design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated. |
prefix |
Character string to add to beginning of column names. |
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
|
If design
is NULL
and grp
is given, design will be calculated as
model.matrix(~0+grp)
. However, grp
isn't needed if design
is provided & add.means
is FALSE
.
Data frame.
McCarthy DJ & Smyth GK (2009). Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25, 765-771.
lmFit
; eBayes
.
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