roast_cor | R Documentation |
Test association of gene sets to phenotype using rotation testing with
roast
using limma 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. See example in vignette of roast_contrasts
.
roast_cor(
object,
G,
feat.tab = NULL,
name = NA,
phenotype = NULL,
design = NULL,
fun = c("fry", "mroast"),
set.statistic = "mean",
weights = NA,
gene.weights = NULL,
trend = FALSE,
block = NULL,
correlation = NULL,
prefix = NULL,
adjust.method = "BH",
min.nfeats = 3,
max.nfeats = 1000,
alternative = c("two.sided", "less", "greater"),
nrot = 999,
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. |
name |
Name for the folder and Excel file that get written. Set to |
phenotype |
Numeric vector of sample characteristics (e.g. phenotypes or treatments).
Should be same length as |
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 |
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
|
prefix |
Character string to add to beginning of column names. |
adjust.method |
Method used to adjust the p-values for multiple testing. Options, in increasing conservatism,
include |
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. |
alternative |
Alternative hypothesis; must be one of |
nrot |
Number of rotations used to estimate the p-values for |
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.
roast_contrasts
.
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