run.limma.matrix | R Documentation |
run limma, given an expression matrix
run.limma.matrix( xdata, xlabel, batch = NULL, out.prefix = NULL, ncell.downsample = NULL, T.fdr = 0.05, T.logFC = 1, T.expr = 0.3, T.bin.useZ = T, verbose = 0, n.cores = NULL, group = NULL, gid.mapping = NULL, do.voom = F, rn.seed = 9999 )
xdata |
data frame or matrix; rows for genes and columns for samples |
xlabel |
factor; cluster label of the samples, with length equal to the number of columns in xdata |
batch |
factor; covariate. (default: NULL) |
out.prefix |
character; if not NULL, write the result to the file(s). (default: NULL) |
ncell.downsample |
integer; for each group, number of cells downsample to. (default: NULL) |
T.fdr |
numeric; threshold of the adjusted p value of moderated t-test (default: 0.05) |
T.logFC |
numeric; threshold of the absoute diff (default: 1) |
T.expr |
numeric; threshold for binarizing exprs (default: 0.3) |
T.bin.useZ |
logical; wheter use the z-score version of assay.namme for binarizing exprs (default: T) |
verbose |
integer; verbose (default: 0) |
n.cores |
integer; number of cores used, if NULL it will be determined automatically (default: NULL) |
group |
character; group of interest, if NULL the last group will be used (default: NULL) |
gid.mapping |
named character; gene id to gene symbol mapping. (default: NULL) |
do.voom |
logical; perform voom transfromation (default: FALSE) |
rn.seed |
integer; random number seed (default: 9999) |
diffeerentially expressed genes dectection using limma
a matrix with dimention as input ( samples in rows and variables in columns)
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