estimateDEPerCellTypeInner | R Documentation |
Differential expression using different methods (deseq2, edgeR, wilcoxon, ttest) with various covariates
estimateDEPerCellTypeInner( raw.mats, cell.groups = NULL, s.groups = NULL, ref.level = NULL, target.level = NULL, common.genes = FALSE, cooks.cutoff = FALSE, min.cell.count = 10, max.cell.count = Inf, independent.filtering = TRUE, n.cores = 4, return.matrix = TRUE, fix.n.samples = NULL, verbose = TRUE, test = "Wald", meta.info = NULL, gene.filter = NULL )
raw.mats |
list of counts matrices; column for gene and row for cell |
cell.groups |
factor specifying cell types (default=NULL) |
s.groups |
list of two character vector specifying the app groups to compare (default=NULL) |
ref.level |
reference level in 'sample.groups', e.g., ctrl, healthy, wt (default=NULL) |
target.level |
target level in 'sample.groups' (default=NULL) |
common.genes |
boolean Only investigate common genes across cell groups (default=FALSE) |
cooks.cutoff |
boolean cooksCutoff for DESeq2 (default=FALSE) |
min.cell.count |
numeric Minimum cell count (default=10) |
max.cell.count |
numeric Maximum cell count (default=Inf). If Inf, there is no limit set. |
independent.filtering |
boolean independentFiltering for DESeq2 (default=FALSE) |
n.cores |
numeric Number of cores (default=1) |
return.matrix |
Return merged matrix of results (default=TRUE) |
fix.n.samples |
Number of samples to fix (default=NULL). If greater the the length of the s.groups, an error is thrown. |
verbose |
boolean Whether to output verbose messages (default=TRUE) |
test |
DE method: deseq2, edgeR, wilcoxon, ttest |
meta.info |
dataframe with possible covariates; for example, sex or age |
gene.filter |
(default=NULL) |
differential expression for each cell type
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