This function replaces a string or regular expression in a feature
variable using the sub
function.
fDataToUnknown(object, fcol = "markers", from = "^$", to = "unknown", ...)
An instance of class MSnSet
.
Feature variable to be modified. Default is
"markers"
. If NULL
, all feature variables will
updated.
A character
defining the string or regular
expression of the pattern to be replaced. Default is the empty
string, i.e. the regular expression "^$"
. See
sub
for details. If NA
, then NA
values are replaced by to
.
A replacement for matched pattern. Default is
"unknown"
. See sub
for details.
Additional arguments passed to sub
.
An updated MSnSet
.
library("pRolocdata")
data(dunkley2006)
getMarkers(dunkley2006, "markers")
#> organelleMarkers
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 14 45 28 55 46
#> Plastid Ribosome TGN unknown vacuole
#> 20 19 13 428 21
dunkley2006 <- fDataToUnknown(dunkley2006,
from = "unknown", to = "unassigned")
getMarkers(dunkley2006, "markers")
#> organelleMarkers
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 14 45 28 55 46
#> Plastid Ribosome TGN unassigned vacuole
#> 20 19 13 428 21