View source: R/roast_contrasts.R
roast_contrasts | R Documentation |
Test contrasts of gene sets using roast
with functions mroast
or fry
. It
returns a data frame with statistics per gene set, and writes this to an Excel file. The Excel file links to
CSV files, which contain statistics per gene set. Some of the arguments only apply to mroast
. See
examples in vignette.
roast_contrasts(
object,
G,
feat.tab,
grp = NULL,
contrast.v,
design = NULL,
fun = c("fry", "mroast"),
set.statistic = "mean",
name = NA,
weights = NA,
gene.weights = NULL,
trend = FALSE,
block = NULL,
correlation = NULL,
adjust.method = "BH",
min.nfeats = 3,
max.nfeats = 1000,
nrot = 999,
alternative = c("two.sided", "less", "greater"),
check.names = TRUE,
pwy.nchar = 199,
seed = 0
)
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 |
feat.tab |
Table of feature (e.g. gene) statistics that the Excel table can link to. |
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. |
fun |
Function to use, either |
set.statistic |
Summary set statistic. Possibilities are |
name |
Name for the folder and Excel file that get written. Set to |
weights |
Non-negative observation weights. Can be a numeric matrix of individual weights of same size as the
|
gene.weights |
Numeric vector of directional (positive or negative) genewise weights. These represent each
gene's contribution to pathways. They are not for precision weights, from |
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. Only for |
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. |
nrot |
Number of rotations used to estimate the p-values for |
alternative |
Alternative hypothesis; must be one of |
check.names |
Logical; should |
pwy.nchar |
Numeric maximum number of characters allowed in pathway name. |
seed |
Integer seed to set for reproducility if |
Pathway (i.e. gene set) names are altered to be valid filenames in Windows and Linux. Numeric columns are rounded to 8 significant figures.
This function does not accept ndups
nor spacing
, because we found that these arguments do not impact
limma::mroast
nor limma::fry
.
Data frame of gene set statistics.
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