Do differential expression for each cell type in a conos object between the specified subsets of apps
Do differential expression for each cell type in a conos object between the specified subsets of apps
getPerCellTypeDE( con.obj, groups = NULL, sample.groups = NULL, cooks.cutoff = FALSE, ref.level = NULL, min.cell.count = 10, remove.na = TRUE, max.cell.count = Inf, test = "LRT", independent.filtering = FALSE, n.cores = 1, cluster.sep.chr = "<!!>", return.details = TRUE )
con.obj |
conos object |
groups |
factor specifying cell types (default=NULL) |
sample.groups |
a list of two character vector specifying the app groups to compare (default=NULL) |
cooks.cutoff |
boolean cooksCutoff for DESeq2 (default=FALSE) |
ref.level |
the reference level of the sample.groups against which the comparison should be made (default=NULL). If NULL, will pick the first one. |
min.cell.count |
integer Minimal number of cells per cluster for a sample to be taken into account in a comparison (default=10) |
remove.na |
boolean If TRUE, remove NAs from DESeq calculations, which often arise as comparisons not possible (default=TRUE) |
max.cell.count |
maximal number of cells per cluster per sample to include in a comparison (useful for comparing the number of DE genes between cell types) (default=Inf) |
test |
which DESeq2 test to use (options: "LRT" or "Wald") (default="LRT") |
independent.filtering |
boolean independentFiltering for DESeq2 (default=FALSE) |
n.cores |
numeric Number of cores (default=1) |
cluster.sep.chr |
character string of length 1 specifying a delimiter to separate cluster and app names (default='<!!>') |
return.details |
boolean Whether to return verbose details (default=TRUE) |
A list of differential expression results for every cell type
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