deconvo_ref | R Documentation |
Estimate the fraction of cell types using defined reference genes
deconvo_ref(
eset,
project = NULL,
arrays = TRUE,
method = "svr",
perm = 100,
reference,
scale_reference = TRUE,
absolute.mode = FALSE,
abs.method = "sig.score"
)
eset |
expression data with matched gene id of reference |
project |
project name used to distinguish different datasets |
arrays |
a logical value. If TRUE, the columns of the input data will be normalized to have the same quantiles. |
method |
deconvolution method. must be "svr" or "lsei" |
perm |
permutation to run svr |
reference |
immune cell gene matrix; eg lm22, lm6 or can be generate using generateRef/generateRef_rnaseq |
scale_reference |
a logical value indicating whether the reference be scaled or not. If TRUE, the value in reference file will be centered and scaled in row direction. |
absolute.mode |
absolute.mode, default is FALSE |
abs.method |
abs.method, default is sig.score |
Dongqiang Zeng
Rongfang Shen
# Loading TCGA-STAD expresion data(raw count matrix)
data(eset_stad, package = "IOBR")
eset <- count2tpm(countMat = eset_stad, source = "local", idType = "ensembl")
deconvo_ref(eset = eset, reference = lm22)
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