This function is a wrapper function around
QFeatures::aggregateFeatures.
It allows the user to provide multiple assays for which
aggregateFeatures
will be applied sequentially.
aggregateFeaturesOverAssays(object, i, fcol, name, fun, ...)
A QFeatures
object
A numeric(1)
or character(1)
indicating which assay
to transfer the colData
to.
The feature variables for each assays i
defining how
to summarise the QFeatures. If fcol
has length 1, the
variable name is assumed to be the same for all assays
A character()
naming the new assay. name
must have
the same length as i
. Note that the function will fail if of
the names in name
is already present.
A function used for quantitative feature aggregation.
Additional parameters passed the fun
.
A QFeatures
object
QFeatures::aggregateFeatures
data("scp1")
scp1 <- aggregateFeaturesOverAssays(scp1,
i = 1:3,
fcol = "peptide",
name = paste0("peptides", 1:3),
fun = colMeans,
na.rm = TRUE)
#>
Aggregated: 1/3
#>
Aggregated: 2/3
#>
Aggregated: 3/3
scp1
#> An instance of class QFeatures containing 8 assays:
#> [1] 190321S_LCA10_X_FP97AG: SingleCellExperiment with 166 rows and 11 columns
#> [2] 190222S_LCA9_X_FP94BM: SingleCellExperiment with 176 rows and 11 columns
#> [3] 190914S_LCB3_X_16plex_Set_21: SingleCellExperiment with 215 rows and 16 columns
#> ...
#> [6] peptides1: SingleCellExperiment with 164 rows and 11 columns
#> [7] peptides2: SingleCellExperiment with 172 rows and 11 columns
#> [8] peptides3: SingleCellExperiment with 214 rows and 16 columns