PTXQC-package	PTXQC-package
%+%	grapes-plus-grapes
alignmentCheck	alignmentCheck
appendEnv	appendEnv
assembleMZQC	assembleMZQC
assignBlocks	assignBlocks
boxplotCompare	boxplotCompare
brewer.pal.Safe	brewer.pal.Safe
byX	byX
byXflex	byXflex
checkEnglishLocale	checkEnglishLocale
computeMatchRTFractions	computeMatchRTFractions
correctSetSize	correctSetSize
createReport	createReport
createYaml	createYaml
CV	CV
darken	darken
del0	del0
delLCP	delLCP
delLCS	delLCS
FilenameMapper	FilenameMapper-class
FilenameMapper-class	FilenameMapper-class
findAlignReference	findAlignReference
fixCalibration	fixCalibration
flattenList	flattenList
getAbundanceClass	getAbundanceClass
getECDF	getECDF
getFileEncoding	getFileEncoding
getFragmentErrors	getFragmentErrors
getHTMLTable	getHTMLTable
getMaxima	getMaxima
getMetaData	getMetaData
getMetaFilenames	getMetaFilenames
getMetricsObjects	getMetricsObjects
getMQPARValue	getMQPARValue
getPCA	getPCA
getPeptideCounts	getPeptideCounts
getProteinCounts	getProteinCounts
getQCHeatMap	getQCHeatMap
getReportFilenames	getReportFilenames
getRunQualityTemplate	getRunQualityTemplate
ggAxisLabels	ggAxisLabels
ggText	ggText
grepv	grepv
idTransferCheck	idTransferCheck
inMatchWindow	inMatchWindow
lcpCount	lcpCount
LCS	LCS
lcsCount	lcsCount
LCSn	LCSn
longestCommonPrefix	longestCommonPrefix
longestCommonSuffix	longestCommonSuffix
modsToTable	modsToTable
modsToTableByRaw	modsToTableByRaw
mosaicize	mosaicize
MQDataReader	MQDataReader-class
MQDataReader-class	MQDataReader-class
MzTabReader	MzTabReader-class
MzTabReader-class	MzTabReader-class
pasten	pasten
pastet	pastet
peakSegmentation	peakSegmentation
peakWidthOverTime	peakWidthOverTime
plotTable	plotTable
plotTableRaw	plotTableRaw
plot_CalibratedMSErr	plot_CalibratedMSErr
plot_Charge	plot_Charge
plot_ContEVD	plot_ContEVD
plot_ContsPG	plot_ContsPG
plot_ContUser	plot_ContUser
plot_ContUserScore	plot_ContUserScore
plot_CountData	plot_CountData
plot_DataOverRT	plot_DataOverRT
plot_IDRate	plot_IDRate
plot_IDsOverRT	plot_IDsOverRT
plot_IonInjectionTimeOverRT	plot_IonInjectionTimeOverRT
plot_MBRAlign	plot_MBRAlign
plot_MBRgain	plot_MBRgain
plot_MBRIDtransfer	plot_MBRIDtransfer
plot_MissedCleavages	plot_MissedCleavages
plot_MS2Decal	plot_MS2Decal
plot_MS2Oversampling	plot_MS2Oversampling
plot_peptideMods	plot_peptideMods
plot_RatiosPG	plot_RatiosPG
plot_RTPeakWidth	plot_RTPeakWidth
plot_ScanIDRate	plot_ScanIDRate
plot_TIC	plot_TIC
plot_TopN	plot_TopN
plot_TopNoverRT	plot_TopNoverRT
plot_UncalibratedMSErr	plot_UncalibratedMSErr
pointsPutX	pointsPutX
print.PTXQC_table	print.PTXQC_table
printWithFooter	printWithFooter
PTXQC	PTXQC
QCMetaFilenames	QCMetaFilenames
qcMetric	qcMetric-class
qcMetric-class	qcMetric-class
qcMetric_MSMSScans_TopNoverRT	qcMetric_MSMSScans_TopNoverRT-class
qcMetric_MSMSScans_TopNoverRT-class	qcMetric_MSMSScans_TopNoverRT-class
qualBestKS	qualBestKS
qualCentered	qualCentered
qualCenteredRef	qualCenteredRef
qualGaussDev	qualGaussDev
qualHighest	qualHighest
qualLinThresh	qualLinThresh
qualMedianDist	qualMedianDist
qualUniform	qualUniform
read.MQ	read.MQ
renameFile	renameFile
repEach	repEach
RSD	RSD
RTalignmentTree	RTalignmentTree
scale01linear	scale01linear
scale_x_discrete_reverse	scale_x_discrete_reverse
scale_y_discrete_reverse	scale_y_discrete_reverse
ScoreInAlignWindow	ScoreInAlignWindow
shortenStrings	shortenStrings
simplifyNames	simplifyNames
supCount	supCount
theme_blank	theme_blank
thinOut	thinOut
thinOutBatch	thinOutBatch
wait_for_writable	wait_for_writable
YAMLClass	YAMLClass-class
YAMLClass-class	YAMLClass-class
