| resDS {muscat} | R Documentation |
resDS provides a simple wrapper to format cluster-level
differential testing results into an easily filterable table, and
to optionally append gene expression frequencies by cluster-sample
& -group, as well as cluster-sample-wise CPM.
resDS(
x,
y,
bind = c("row", "col"),
frq = FALSE,
cpm = FALSE,
digits = 3,
sep = "__",
...
)
x |
|
y |
|
bind |
character string specifying the output format (see details). |
frq |
logical or a pre-computed list of expression frequencies
as returned by |
cpm |
logical specifying whether CPM by cluster-sample should be appendeded to the output result table(s). |
digits |
integer value specifying the number of significant digits to maintain. |
sep |
character string to use as separator when constructing new column names. |
... |
optional arguments passed to
|
When bind = "col", the list of DS testing results at
y$table will be merge vertically (by column) into a single table
in tidy format with column contrast/coef specifying the comparison.
Otherwise, when bind = "row", an identifier of the respective
contrast or coefficient will be appended to the column names,
and all tables will be merge horizontally (by row).
Expression frequencies pre-computed with calcExprFreqs
may be provided with frq. Alternatively, when frq = TRUE,
expression frequencies can be computed directly, and additional arguments
may be passed to calcExprFreqs (see examples below).
returns a 'data.frame'.
Helena L Crowell & Mark D Robinson
data(sce) # compute pseudobulks (sum of counts) pb <- aggregateData(sce, assay = "counts", fun = "sum") # run DS analysis (edgeR on pseudobulks) res <- pbDS(pb, method = "edgeR") head(resDS(sce, res, bind = "row")) # tidy format head(resDS(sce, res, bind = "col", digits = Inf)) # append CPMs & expression frequencies head(resDS(sce, res, cpm = TRUE)) head(resDS(sce, res, frq = TRUE)) # pre-computed expression frequencies & append frq <- calcExprFreqs(sce, assay = "counts", th = 0) head(resDS(sce, res, frq = frq))