countUniqueFeatures {QFeatures} | R Documentation |
Count Unique Features
This function counts the number of unique features per sample. A
grouping structure can be provided to count higher level features
from assays, for example counting the number of unique proteins
from PSM data.
Description
Count Unique Features
This function counts the number of unique features per sample. A
grouping structure can be provided to count higher level features
from assays, for example counting the number of unique proteins
from PSM data.
Usage
countUniqueFeatures(object, i, groupBy = NULL, colDataName = "count")
Arguments
object |
An object of class QFeatures .
|
i |
A numeric() or character() vector indicating from
which assays the rowData should be taken.
|
groupBy |
A character(1) indicating the variable name in
the rowData that contains the grouping variable, for
instance to count the unique number of peptides or proteins
expressed in each samples (column). If groupBy is missing,
the number of non zero elements per sample will be stored.
|
colDataName |
A character(1) giving the name of the new
variable in the colData where the number of unique features
will be stored. The name cannot already exist in the
colData .
|
Value
An object of class QFeatures
.
Examples
data("ft_na")
## Count number of (non-missing) PSMs
ft_na <- countUniqueFeatures(ft_na,
i = "na",
colDataName = "counts")
ft_na$counts
## Count number of unique rowData feature
ft_na <- countUniqueFeatures(ft_na,
i = "na",
groupBy = "Y",
colDataName = "Y_counts")
ft_na$Y_counts
[Package
QFeatures version 1.2.0
Index]