peptideSet-methods: peptideSet methods

Description Accessors Display Subset

Description

Methods for handling peptideSet objects

Accessors

nrow(x):

The number of peptides in x.

ncol(x):

The number of samples in x.

start(x):

Get the starts of the peptides.

end(x):

Get the ends of the peptides.

width(x):

Get the widths of the peptides.

position(x):

Get the coordinates of the central amino-acid of each peptide, given by: round((start(x) + end(x))/2).

ranges(x):

Returns a GRanges object that contains the annotations for the peptides.

ranges(x)<- value

Set annotations for the peptides.

values(x):

Returns a SplitDataFrameList. Accessor for the values of the featureRange slot.

clade(x):

If available, returns the clade information for each peptide as a matrix.

peptide(x):

Get the sequence of the peptides.

peptide(x) <- value

Set the sequence of the peptides.

featureID(x):

Get the ID of the peptides.

pepZscore(x):

If available, returns a matrix of the zScores for each peptide.

pepZscore(x) <- value

Set the zScores for each peptide

Display

show(object):

Display a peptideSet object.

summary(object):

Summarize a peptideSet object.

Subset

x[i, j]:

Subset x by peptides (i), or samples (j).

subset(x, subset, drop=FALSE):

Subset x given an expression 'subset'.


pepStat documentation built on April 29, 2020, 5:19 a.m.