SilacProteomicsExperiment-accessors {pulsedSilac} | R Documentation |
All the accessors, dimension, subsetting, merging and coercers
that work on SilacProteomicsExperiment
objects. Since the
SilacProteomicsExperiment
object has both protein and peptide level data,
most of the functions have a 'Prot' or 'Pept' suffix to indicate which
level should be used. If the non-suffix function is used, then a list with
both protein and peptide data is returned.
These functions also work on SilacProteinExperiment
and SilacPeptideExperiment
objects.
PeptExp(x) ProtExp(x) ## S4 method for signature 'SilacProteomicsExperiment' assayNames(x, ..., withDimnames) ## S4 method for signature 'SilacProteinExperiment' assayNamesProt(x) ## S4 replacement method for signature 'SilacProteinExperiment' assayNamesProt(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' assayNamesProt(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' assayNamesProt(x) <- value ## S4 method for signature 'SilacPeptideExperiment' assayNamesPept(x) ## S4 replacement method for signature 'SilacPeptideExperiment' assayNamesPept(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' assayNamesPept(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' assayNamesPept(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' assays(x, withDimnames = TRUE, ...) ## S4 method for signature 'SilacProteinExperiment' assaysProt(x) ## S4 replacement method for signature 'SilacProteinExperiment' assaysProt(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' assaysProt(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' assaysProt(x) <- value ## S4 method for signature 'SilacPeptideExperiment' assaysPept(x) ## S4 replacement method for signature 'SilacPeptideExperiment' assaysPept(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' assaysPept(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' assaysPept(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' cbind(..., deparse.level = 1) ## S4 method for signature 'SilacProteomicsExperiment' colData(x, ...) ## S4 replacement method for signature 'SilacProteomicsExperiment,ANY' colData(x, ...) <- value ## S4 method for signature 'SilacProteomicsExperiment' colnames(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' colnames(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' dim(x) ## S4 method for signature 'SilacProteomicsExperiment' x$name ## S4 replacement method for signature 'SilacProteomicsExperiment' x$name <- value ## S4 method for signature 'SilacProteomicsExperiment' length(x) ## S4 method for signature 'SilacProteomicsExperiment' linkerDf(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' linkerDf(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' metadata(x, ...) ## S4 replacement method for signature 'SilacProteomicsExperiment' metadata(x, ...) <- value ## S4 method for signature 'SilacProteomicsExperiment' metaoptions(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' metaoptions(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' ncol(x) ## S4 method for signature 'SilacProteomicsExperiment' rbind(..., deparse.level = 1) ## S4 method for signature 'SilacProteomicsExperiment' rowData(x, use.names = TRUE, ...) ## S4 replacement method for signature 'SilacProteomicsExperiment' rowData(x, ...) <- value ## S4 method for signature 'SilacProteinExperiment' rowDataProt(x) ## S4 replacement method for signature 'SilacProteinExperiment' rowDataProt(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' rowDataProt(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' rowDataProt(x) <- value ## S4 method for signature 'SilacPeptideExperiment' rowDataPept(x) ## S4 replacement method for signature 'SilacPeptideExperiment' rowDataPept(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' rowDataPept(x) ## S4 method for signature 'SilacProteomicsExperiment' rownamesProt(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' rownamesProt(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' rownamesPept(x) ## S4 replacement method for signature 'SilacProteomicsExperiment' rownamesPept(x) <- value ## S4 method for signature 'SilacProteomicsExperiment' subset(x, ...) ## S4 method for signature 'SilacProteinExperiment' subsetProt(x, ...) ## S4 method for signature 'SilacProteomicsExperiment' subsetProt(x, ...) ## S4 method for signature 'SilacPeptideExperiment' subsetPept(x, ...) ## S4 method for signature 'SilacProteomicsExperiment' subsetPept(x, ...) ## S4 method for signature 'SilacProteomicsExperiment,ANY,ANY,ANY' x[i, j, ..., drop = TRUE]
x |
A |
... |
For |
withDimnames |
Unused. |
value |
An object of class specified in the S4 method signature or as described in the following sections. |
deparse.level |
Unused. |
name |
Column name of colData. |
use.names |
Unused. |
i, j |
For |
drop |
A |
Elements from a SilacProteomicsExperiment
object.
The following functions can be used to access the data in the class slots
assays
, assaysProt
, assaysPept
:Access the assays (list of matrices) of the object. Value should be a matrix or list of matrices.
assayNames
, assayNamesProt
, assayNamesPept
:Access the assay names of the object. Value should be a character vector.
rowData
, rowDataProt
, rowDataPept
:Access the
protein/peptide feature data.frame
of the object. Value should be a
data.frame
with as many rows as proteins/peptides.
colData
:Access the samples data.frame
of the object.
Value should be a data.frame
with as many rows as samples.
metadata
:Access the metadata list
of the object.
Value should be a list
.
metaoptions
:Access the metaoptions list
of the
object. Value should be a list
.
linkerDf
:Access the linker data.frame
of the object
(only ProteomicsExperiment). Value should be a data.frame
output
from buildLinkerDf
.
ProtExp
and PeptExp
:Access the experiment objects
in a SilacProteomicsExperiment
.
The following functions can be used to get the number of proteins/peptides and number of samples:
nrow
:Gives how many proteins and peptides the object has.
ncol
:Gives how many samples the object has.
dim
:Gives both the number of proteins andpeptides and the number of samples the object has.
length
:Gives how many proteins and or peptides the object has.
The following functions can be used to subset the different classes:
$
:Gives a column from colData by name.
`[`
:Can be used to subset by row and column.
subset
, subsetProt
and subsetPept
:Allows
to subset based on a logical comparison using a column name from the
rowData data.frame
.
The ProteomicsExperiment class is a bit more complex since there are two levels at which the subset can be done and these two levels can be linked or not.
If the metaoption 'linkedSubset' is TRUE, then when subsetting on one level, the proteins/peptide linked to such level are also subsetted. Otherwise, one of the levels remains unmodified.
subsetProt
can be used to apply subset
at the rowData
data.frame
of the protein level. subsetProt
can be used to
apply subset
at the rowData data.frame
of the peptide level. If
subset
is used, then subsetProt
or subsetPept
will be
used depending on the metaoption 'subsetMode'.
'[' acts in the same manner as calling subset
. In this case numerics
are used and samples can also be selected.
The vignette offers a detailed set of simple examples with all the possible cases.
The following functions can be used to aggregate objects of the same class together:
cbind
:Joins two or more objects horizontally (adding samples). Must have the same proteins/peptides and in the same order.
rbind
:Joins two or more objects vertically (adding proteins/peptides). Must have the same samples and in the same order.
merge
:Joins two objects by adding new samples and tries
to merge the proteins/peptide rowData data.frames and recalculate the
linkerDf data.frame
for the SilacProteomicsExperiment
class.
Merge methods are explained in detail in merge.
# Accessors ## assays data('wormsPE') assays(wormsPE) assaysProt(wormsPE) assaysPept(wormsPE) ## assaysNames assayNames(wormsPE) assayNamesProt(wormsPE) assayNamesPept(wormsPE) ## colData colData(wormsPE) ## rowData rowData(wormsPE) rowDataProt(wormsPE) rowDataPept(wormsPE) ## metadata metadata(wormsPE) ## metaoptions #metaoptions(wormsPE) ## linkerDf linkerDf(wormsPE) # Dimensions and dimensions names nrow(wormsPE) ncol(wormsPE) dim(wormsPE) length(wormsPE) colnames(wormsPE) rownamesProt(wormsPE) rownamesPept(wormsPE) # Subsetting wormsPE$line wormsPE[1,1] subsetProt(wormsPE, protein_id == 'AC3.2') subsetPept(wormsPE, Sequence == 'AIQEISDYHFLIK') # Merging rbind(wormsPE[1:10, ], wormsPE[11:20, ]) cbind(wormsPE[,1:2], wormsPE[,3:4]) #merge(wormsPE[1:10, 1:3], wormsPE[3:10, 4:5])