NEWS.md
chromatogram()
method.readMgfData()
(see issue 597).calculateFragments
for neutral losses with a charge > 1 (see issue 573).plot
with type = "XIC"
to create an empty plot for samples without data points (issue #549).calculateFragments
man page (see issue #537).impute,MSnSet-method
with MsCoreUtils::impute_matrix()
.normalise,MSnSet-method
with MsCoreUtils::normalize_matrix()
.ReporterIons
class using TMT16.formatRt()
using MsCoreUtils::formatRt()
.MsCoreUtils::robustSummary()
(deleted code in this package).MsCoreUtils::medianPolish()
.normalize,Chromatogram
method.filterIntensity,Chromatogram
method.align,Chromatogram
method.extractSpectraData
function to extract all data from an MSnExp
or Spectra
object as a DataFrame
to be used with the Spectra
package.check.names
in read.delim
is now (internally) set to FALSE
. This will make it easier to write MzTab objects back to files. See issue #501 for a discussion.readSRMData
(issue #486) which caused the function to not discriminate between chromatograms with different precursor collision energy.pickPeaks
: set variable centroided
only to TRUE
for spectra matching the provided msLevel.
.msLevel.
to smooth
.consensusSpectrum
: add parameter mzFun
allowing to define the aggregation function for m/z values, change default for mzd
to 0
(hence avoid estimating m/z differences by default) and change the default for parameter intensityFun
to median
.weighted
to consensusSpectrum
and change the default from reporting the intensity-weighted mean of m/z values for consensus peaks to reporting the m/z of the largest peak <2019-09-12 Thu>.msLevel
to pickPeaks
to allow peak picking in specific MS levels. See #478 <2019-09-04 Wed>.filterMsLevel,
filterMz,
filterPolarity,
filterRt,
filterAcquisitionNum,
filterEmptySpectra,
filterPrecursorScan,
productMz,
filterPrecursorMzand
filterIsolationWindowgenerics from
ProtGenerics`.plot,Spectrum,Spectrum
now also supports MS1 spectra (see #477) <2019-07-23 Tue>isolationWindowLowerMz
and isolationWindowUpperMz
methods <2019-04-15 Mon>filterPrecursorMz
method <2019-04-15 Mon>filterIsolationWindow
method <2019-05-16 Tue>timeDomain
in combineSpectra
and combineSpectraMovingWindow
to FALSE
<2018-10-18 Thu>consensusSpectrum
<2018-10-24 Wed>combineFeatures
contributed by Ludger Goeminne, Adriaan Sticker and Lieven Clement <2018-04-03 Tue>utils.removePeaks
to new IRanges
implementation; thanks to H. Pagès for the implementation (see PR #320 for discussion) <2018-03-26>.timeDomain
to combineSpectra
, combineSpectraMovingWindow
and estimateMzScattering
allowing to perform the grouping of m/z values from consecutive scans based on the square root of the m/z values <2018-03-29>.phenoData<-
method for pSet
(issue #299 <2018-01-22>.featureData
slot, accessible with fData
to store metadata for the individial MSnSets of the list. MSnSetList
also not has an sapply
method. <2018-01-10 Wed>fcol
argument (see issue #195) <2018-01-11 Thu>MSnExp
and OnDiskMSnExp
; closes issue #282 and PR #287 <2017-12-16 Sat>.fastquant_max
to get little speed improvents for isobaric quantification (see PR #280) <2017-11-27 Mon>.protocolData
in isobaric quantification; fixes #265
isCentroidedFromFile
function <2017-08-11 Fri>calculateFragments
now just calculate fragments for all n - 1L
bonds (before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun>isEmpty
methods for Chromatogram
and Chromatograms
objects <2017-09-05 Tue>getColsFromPattern
and getRowsFromPattern
and add unit tests <2017-05-11 Thu>..filterNA
and rewrite filterNA
for matrix
and MSnSet
<2017-05-11 Thu>.naplot
gains a reorderRows
and reorderColumns
argument <2017-06-05 Mon>.utils.clean
. It now keeps just the zeros in the direct neighbourhood (see #210) <2017-05-04 Thu>.getTopIdx
and subsetById
are replaced by .topIdx
. See PR #199 for details. <2017-03-20 Mon>calculateFragments
; closes #200 <2017-03-22 Wed>diff.median
normalisation for MSnSet
s. <2017-01-26 Thu>cex
, lwd
, pch
for peaks and fragments in plot,Spectrum,Spectrum-method; closes #148 <2016-08-12 Fri>added a readMSnSet function [2011-09-08 Thu]
added a write.MSnSet(“MSnSet”) method [2011-09-08 Thu]
vignette/man updates - mainly data import section documenting readMSData and readMgfData [2011-09-08 Thu]
incorporating mzR io frame work [2011-09-05 Mon]
use mzR’s peaksCount and header generics [2011-09-05 Mon]
added test to check that readMzXMLData and readMSData give same output [2011-09-05 Mon]
added readMSData.Rd doc file [2011-09-05 Mon]
added Author@R field in DESCRIPTION [2011-09-07 Wed]
compressed/resaved (using resaveRdaFiles) itraqdata.RData file to [2011-09-07 Wed]