resDS | 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 |
a |
y |
a list of DS testing results as returned
by |
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
# compute pseudobulks (sum of counts) data(example_sce) pb <- aggregateData(example_sce, assay = "counts", fun = "sum") # run DS analysis (edgeR on pseudobulks) res <- pbDS(pb, method = "edgeR") head(resDS(example_sce, res, bind = "row")) # tidy format head(resDS(example_sce, res, bind = "col", digits = Inf)) # append CPMs & expression frequencies head(resDS(example_sce, res, cpm = TRUE)) head(resDS(example_sce, res, frq = TRUE)) # pre-computed expression frequencies & append frq <- calcExprFreqs(example_sce, assay = "counts", th = 0) head(resDS(example_sce, res, frq = frq))
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