Compare two cell types across the entire panel
Compare two cell types across the entire panel
getBetweenCellTypeDE( con.obj, groups = NULL, sample.groups = NULL, cooks.cutoff = FALSE, refgroup = NULL, altgroup = NULL, min.cell.count = 10, independent.filtering = FALSE, cluster.sep.chr = "<!!>", return.details = TRUE, only.paired = TRUE, remove.na = TRUE )
con.obj |
conos object |
groups |
factor describing cell grouping (default=NULL) |
sample.groups |
a named list of two character vectors specifying the app groups to compare (default=NULL) |
cooks.cutoff |
boolean cooksCutoff parameter for DESeq2 (default=FALSE) |
refgroup |
cell type to compare to be used as reference (default=NULL) |
altgroup |
cell type to compare to be used as ALT against refgroup (default=NULL) |
min.cell.count |
numeric Minimum number of cells per celltype/sample combination to keep (default=10) |
independent.filtering |
boolean Whether to use independentFiltering parameter for DESeq2 (default=FALSE) |
cluster.sep.chr |
character string of length 1 specifying a delimiter to separate cluster and app names (default='<!!>') |
return.details |
boolean Return detailed results (default=TRUE) |
only.paired |
boolean Only keep samples that that both cell types above the min.cell.count threshold (default=TRUE) |
remove.na |
boolean If TRUE, remove NAs from DESeq calculations (default=TRUE) |
Returns either a DESeq2::results() object, or if return.details=TRUE, returns a list of the DESeq2::results(), the samples from the panel to use in this comparison, refgroups, altgroup, and samplegroups
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