R/dataDoc.R
In huang704/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
#' Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.
#'
#' Example of Proteome discover PSM sheet.
#' It is the input for PDtoMSstatsTMTFormat function, with annotation file.
#' Annotation file should be made by users.
#' It includes peak intensities for 10 proteins
#' among 15 MS runs with TMT-10plex.
#' The variables are as follows:
#'
#' \itemize{
#' \item Master.Protein.Accessions
#' \item Protein.Accessions
#' \item Annotated.Sequence
#' \item Charge
#' \item Ions.Score
#' \item Spectrum.File
#' \item Quan.Info
#' \item Channels : 126, ..., 131
#' }
#'
#' @format A data frame with 2858 rows and 50 variables.
#' @examples
#' head(raw.pd)
#'
"raw.pd"
#' Example of annotation file for raw.pd,
#' which is the PSM output of Proteome Discoverer
#'
#' Annotation of example data, raw.pd, in this package.
#' It should be prepared by users.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID. It should be the same as Spectrum.File info
#' in raw.pd.
#' \item Channel : Labeling information (126, ... 131). It should be
#' consistent with the channel columns in raw.pd.
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
#' a single mass spectrometry experiment. If the channal doesn't have sample, please add `Empty' under Condition.
#' \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
#' For example, if `TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match
#' with same `Mixture' value.
#' \item Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
#' Then one technical replicate of one mixture should correspond to multuple fractions.
#' For example, if `Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
#' then they should have same `TechRepMixture' and `Mixture' value.
#' \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add `Empty' under BioReplicate.
#' }
#'
#' @format A data frame with 150 rows and 7 variables.
#' @examples
#' head(annotation.pd)
#'
"annotation.pd"
#' Example of output from MaxQuant for TMT-10plex experiments.
#'
#' Example of evidence.txt from MaxQuant.
#' It is the input for MaxQtoMSstatsTMTFormat function, with proteinGroups.txt
#' and annotation file. Annotation file should be made by users.
#' It includes peak intensities for 10 proteins among 15 MS runs with TMT10.
#' The important variables are as follows:
#'
#' \itemize{
#' \item Proteins
#' \item Protein.group.IDs
#' \item Modified.sequence
#' \item Charge
#' \item Raw.file
#' \item Score
#' \item Potential.contaminant
#' \item Reverse
#' \item Channels : Reporter.intensity.corrected.0, ...,
#' Reporter.intensity.corrected.9
#' }
#'
#' @format A data frame with 1075 rows and 105 variables.
#' @examples
#' head(evidence)
#'
"evidence"
#' Example of proteinGroups file from MaxQuant for TMT-10plex experiments.
#'
#' Example of proteinGroup.txt file from MaxQuant,
#' which is identified protein group information file.
#' It is the input for MaxQtoMSstatsTMTFormat function, with evidence.txt
#' and annotation file.
#' It includes identified protein groups for 10 proteins
#' among 15 MS runs with TMT10.
#' The important variables are as follows:
#'
#' \itemize{
#' \item id
#' \item Protein.IDs
#' \item Only.identified.by.site
#' \item Potential.contaminant
#' \item Reverse
#' }
#'
#' @format A data frame with 1075 rows and 105 variables.
#' @examples
#' head(proteinGroups)
#'
"proteinGroups"
#' Example of annotation file for evidence, which is the output of MaxQuant.
#'
#' Annotation of example data, evidence, in this package.
#' It should be prepared by users.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID. It should be the same as Raw.file info
#' in raw.mq
#' \item Channel : Labeling information (channel.0, ..., channel.9).
#' The channel index should be consistent with the channel columns in raw.mq.
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
#' a single mass spectrometry experiment. If the channal doesn't have sample, please add `Empty' under Condition.
#' \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
#' For example, if `TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match
#' with same `Mixture' value.
#' \item Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
#' Then one technical replicate of one mixture should correspond to multuple fractions.
#' For example, if `Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
#' then they should have same `TechRepMixture' and `Mixture' value.
#' \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add `Empty' under BioReplicate.
#' }
#'
#' @format A data frame with 150 rows and 7 variables.
#' @examples
#' head(annotation.mq)
#'
"annotation.mq"
#' Example of output from SpectroMine for TMT-6plex experiments.
#'
#' Example of SpectroMine PSM sheet.
#' It is the output of SpectroMine and the input for SpectroMinetoMSstatsTMTFormat function,
#' with annotation file.
#' Annotation file should be made by users.
#' It includes peak intensities for 10 proteins among 12 MS runs with TMT-6plex.
#' The important variables are as follows:
#'
#' \itemize{
#' \item PG.ProteinAccessions
#' \item P.MoleculeID
#' \item PP.Charge
#' \item R.FileName
#' \item PG.QValue
#' \item PSM.Qvalue
#' \item Channels : PSM.TMT6_126..Raw., ..., PSM.TMT6_131..Raw.
#' }
#'
#' @format A data frame with 170 rows and 28 variables.
#' @examples
#' head(raw.mine)
#'
"raw.mine"
#' Example of annotation file for raw.mine, which is the output of SpectroMine.
#'
#' Annotation of example data, raw.mine, in this package.
#' It should be prepared by users.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID. It should be the same as R.FileName info
#' in raw.mine
#' \item Channel : Labeling information (TMT6_126, ..., TMT6_131).
#' The channels should be consistent with the channel columns in raw.mine.
#' \item Condition : Condition (ex. Healthy, Cancer, Time0). If the channal doesn't have sample, please add 'Empty' under Condition.
#' \item Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
#' a single mass spectrometry experiment.
#' \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
#' For example, if 'TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match
#' with same 'Mixture' value.
#' \item Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
#' Then one technical replicate of one mixture should correspond to multuple fractions.
#' For example, if 'Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
#' then they should have same 'TechRepMixture' and 'Mixture' value.
#' \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add 'Empty' under BioReplicate
#' }
#'
#' @format A data frame with 72 rows and 7 variables.
#' @examples
#' head(annotation.mine)
#'
"annotation.mine"
#' Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.
#'
#' Example of MSstatsTMT PSM sheet from MaxQuant.
#' It is the input for OpenMStoMSstatsTMTFormat function.
#' It includes peak intensities for 10 proteins among 27 MS runs from three TMT10 mixtures.
#' The important variables are as follows:
#'
#' \itemize{
#' \item RetentionTime
#' \item ProteinName
#' \item PeptideSequence
#' \item Charge
#' \item Channel
#' \item Condition
#' \item BioReplicate
#' \item Run
#' \item Mixture
#' \item TechRepMixture
#' \item Fraction
#' \item Intensity
#' \item Reference
#' }
#'
#' @format A data frame with 860 rows and 13 variables.
#' @examples
#' head(raw.om)
#'
"raw.om"
#' Example of output from PDtoMSstatsTMTFormat function
#'
#' It is made from \code{\link{raw.pd}} and \code{\link{annotation.pd}},
#' which is the output of PDtoMSstatsTMTFormat function.
#' It should include the required columns as below.
#' The variables are as follows:
#'
#' \itemize{
#' \item ProteinName : Protein ID
#' \item PeptideSequence : peptide sequence
#' \item Charge : peptide charge
#' \item PSM : peptide ion and spectra match
#' \item Channel : Labeling information (126, ... 131)
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item BioReplicate : Unique ID for biological subject.
#' \item Run : MS run ID
#' \item Mixture : Unique ID for TMT mixture.
#' \item TechRepMixture : Unique ID for technical replicate of one TMT mixture.
#' \item Intensity: Protein Abundance
#' }
#'
#' @format A data frame with 20110 rows and 11 variables.
#' @examples
#' head(input.pd)
#'
"input.pd"
#' Example of output from proteinSummarizaiton function
#'
#' It is made from \code{\link{input.pd}}.
#' It is the output of proteinSummarization function.
#' It should include the required columns as below.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID
#' \item Protein : Protein ID
#' \item Abundance: Protein-level summarized abundance
#' \item Channel : Labeling information (126, ... 131)
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item BioReplicate : Unique ID for biological subject.
#' \item TechRepMixture : Unique ID for technical replicate of one TMT mixture.
#' \item Mixture : Unique ID for TMT mixture.
#' }
#'
#' @format A data frame with 100 rows and 8 variables.
#' @examples
#' head(quant.pd.msstats)
#'
"quant.pd.msstats"
#' Example of output from groupComparisonTMT function
#'
#' It is the output of groupComparisonTMT function,
#' which is the result of group comparions with the output of proteinSummarization function.
#' It should include the columns as below.
#' The variables are as follows:
#'
#' \itemize{
#' \item Protein : Protein ID
#' \item Label: Label of the pairwise comparision or contrast
#' \item log2FC: Log2 fold change
#' \item SE: Standard error of the comparsion of contrast results
#' \item DF: Degree of freedom
#' \item pvalue: Value of p statistic of the test
#' \item adj.pvalue: adjusted p value
#' \item issue: used for indicating the reason why a comparison is not testable. NA means the comparison is testable.
#' 'oneConditionMissing' means the protein has no measurements in one conndition of the comparison.
#' Furtherone, when 'issue = oneConditionMissing', 'log2FC = Inf' means the negative condition
#' (with coefficient -1 in the Label column) is missing and 'log2FC = -Inf' means
#' the positive condition (with coefficient 1 in the Label column) is missing.
#' completeMissing' means the protein has no measurements in all the connditions of the comparison.
#' unfittableModel' means there is no enough measurements to fit the linear model.
#' In other words, each condition has only one measurement.
#' }
#'
#' @format A data frame with 60 rows and 7 variables.
#' @examples
#' head(test.pairwise)
#'
"test.pairwise"
huang704/MSstatsTMT documentation built on Jan. 1, 2021, 3:21 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.
#'
#' Example of Proteome discover PSM sheet.
#' It is the input for PDtoMSstatsTMTFormat function, with annotation file.
#' Annotation file should be made by users.
#' It includes peak intensities for 10 proteins
#' among 15 MS runs with TMT-10plex.
#' The variables are as follows:
#'
#' \itemize{
#' \item Master.Protein.Accessions
#' \item Protein.Accessions
#' \item Annotated.Sequence
#' \item Charge
#' \item Ions.Score
#' \item Spectrum.File
#' \item Quan.Info
#' \item Channels : 126, ..., 131
#' }
#'
#' @format A data frame with 2858 rows and 50 variables.
#' @examples
#' head(raw.pd)
#'
"raw.pd"
#' Example of annotation file for raw.pd,
#' which is the PSM output of Proteome Discoverer
#'
#' Annotation of example data, raw.pd, in this package.
#' It should be prepared by users.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID. It should be the same as Spectrum.File info
#' in raw.pd.
#' \item Channel : Labeling information (126, ... 131). It should be
#' consistent with the channel columns in raw.pd.
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
#' a single mass spectrometry experiment. If the channal doesn't have sample, please add `Empty' under Condition.
#' \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
#' For example, if `TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match
#' with same `Mixture' value.
#' \item Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
#' Then one technical replicate of one mixture should correspond to multuple fractions.
#' For example, if `Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
#' then they should have same `TechRepMixture' and `Mixture' value.
#' \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add `Empty' under BioReplicate.
#' }
#'
#' @format A data frame with 150 rows and 7 variables.
#' @examples
#' head(annotation.pd)
#'
"annotation.pd"
#' Example of output from MaxQuant for TMT-10plex experiments.
#'
#' Example of evidence.txt from MaxQuant.
#' It is the input for MaxQtoMSstatsTMTFormat function, with proteinGroups.txt
#' and annotation file. Annotation file should be made by users.
#' It includes peak intensities for 10 proteins among 15 MS runs with TMT10.
#' The important variables are as follows:
#'
#' \itemize{
#' \item Proteins
#' \item Protein.group.IDs
#' \item Modified.sequence
#' \item Charge
#' \item Raw.file
#' \item Score
#' \item Potential.contaminant
#' \item Reverse
#' \item Channels : Reporter.intensity.corrected.0, ...,
#' Reporter.intensity.corrected.9
#' }
#'
#' @format A data frame with 1075 rows and 105 variables.
#' @examples
#' head(evidence)
#'
"evidence"
#' Example of proteinGroups file from MaxQuant for TMT-10plex experiments.
#'
#' Example of proteinGroup.txt file from MaxQuant,
#' which is identified protein group information file.
#' It is the input for MaxQtoMSstatsTMTFormat function, with evidence.txt
#' and annotation file.
#' It includes identified protein groups for 10 proteins
#' among 15 MS runs with TMT10.
#' The important variables are as follows:
#'
#' \itemize{
#' \item id
#' \item Protein.IDs
#' \item Only.identified.by.site
#' \item Potential.contaminant
#' \item Reverse
#' }
#'
#' @format A data frame with 1075 rows and 105 variables.
#' @examples
#' head(proteinGroups)
#'
"proteinGroups"
#' Example of annotation file for evidence, which is the output of MaxQuant.
#'
#' Annotation of example data, evidence, in this package.
#' It should be prepared by users.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID. It should be the same as Raw.file info
#' in raw.mq
#' \item Channel : Labeling information (channel.0, ..., channel.9).
#' The channel index should be consistent with the channel columns in raw.mq.
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
#' a single mass spectrometry experiment. If the channal doesn't have sample, please add `Empty' under Condition.
#' \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
#' For example, if `TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match
#' with same `Mixture' value.
#' \item Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
#' Then one technical replicate of one mixture should correspond to multuple fractions.
#' For example, if `Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
#' then they should have same `TechRepMixture' and `Mixture' value.
#' \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add `Empty' under BioReplicate.
#' }
#'
#' @format A data frame with 150 rows and 7 variables.
#' @examples
#' head(annotation.mq)
#'
"annotation.mq"
#' Example of output from SpectroMine for TMT-6plex experiments.
#'
#' Example of SpectroMine PSM sheet.
#' It is the output of SpectroMine and the input for SpectroMinetoMSstatsTMTFormat function,
#' with annotation file.
#' Annotation file should be made by users.
#' It includes peak intensities for 10 proteins among 12 MS runs with TMT-6plex.
#' The important variables are as follows:
#'
#' \itemize{
#' \item PG.ProteinAccessions
#' \item P.MoleculeID
#' \item PP.Charge
#' \item R.FileName
#' \item PG.QValue
#' \item PSM.Qvalue
#' \item Channels : PSM.TMT6_126..Raw., ..., PSM.TMT6_131..Raw.
#' }
#'
#' @format A data frame with 170 rows and 28 variables.
#' @examples
#' head(raw.mine)
#'
"raw.mine"
#' Example of annotation file for raw.mine, which is the output of SpectroMine.
#'
#' Annotation of example data, raw.mine, in this package.
#' It should be prepared by users.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID. It should be the same as R.FileName info
#' in raw.mine
#' \item Channel : Labeling information (TMT6_126, ..., TMT6_131).
#' The channels should be consistent with the channel columns in raw.mine.
#' \item Condition : Condition (ex. Healthy, Cancer, Time0). If the channal doesn't have sample, please add 'Empty' under Condition.
#' \item Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
#' a single mass spectrometry experiment.
#' \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
#' For example, if 'TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match
#' with same 'Mixture' value.
#' \item Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
#' Then one technical replicate of one mixture should correspond to multuple fractions.
#' For example, if 'Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
#' then they should have same 'TechRepMixture' and 'Mixture' value.
#' \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add 'Empty' under BioReplicate
#' }
#'
#' @format A data frame with 72 rows and 7 variables.
#' @examples
#' head(annotation.mine)
#'
"annotation.mine"
#' Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.
#'
#' Example of MSstatsTMT PSM sheet from MaxQuant.
#' It is the input for OpenMStoMSstatsTMTFormat function.
#' It includes peak intensities for 10 proteins among 27 MS runs from three TMT10 mixtures.
#' The important variables are as follows:
#'
#' \itemize{
#' \item RetentionTime
#' \item ProteinName
#' \item PeptideSequence
#' \item Charge
#' \item Channel
#' \item Condition
#' \item BioReplicate
#' \item Run
#' \item Mixture
#' \item TechRepMixture
#' \item Fraction
#' \item Intensity
#' \item Reference
#' }
#'
#' @format A data frame with 860 rows and 13 variables.
#' @examples
#' head(raw.om)
#'
"raw.om"
#' Example of output from PDtoMSstatsTMTFormat function
#'
#' It is made from \code{\link{raw.pd}} and \code{\link{annotation.pd}},
#' which is the output of PDtoMSstatsTMTFormat function.
#' It should include the required columns as below.
#' The variables are as follows:
#'
#' \itemize{
#' \item ProteinName : Protein ID
#' \item PeptideSequence : peptide sequence
#' \item Charge : peptide charge
#' \item PSM : peptide ion and spectra match
#' \item Channel : Labeling information (126, ... 131)
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item BioReplicate : Unique ID for biological subject.
#' \item Run : MS run ID
#' \item Mixture : Unique ID for TMT mixture.
#' \item TechRepMixture : Unique ID for technical replicate of one TMT mixture.
#' \item Intensity: Protein Abundance
#' }
#'
#' @format A data frame with 20110 rows and 11 variables.
#' @examples
#' head(input.pd)
#'
"input.pd"
#' Example of output from proteinSummarizaiton function
#'
#' It is made from \code{\link{input.pd}}.
#' It is the output of proteinSummarization function.
#' It should include the required columns as below.
#' The variables are as follows:
#'
#' \itemize{
#' \item Run : MS run ID
#' \item Protein : Protein ID
#' \item Abundance: Protein-level summarized abundance
#' \item Channel : Labeling information (126, ... 131)
#' \item Condition : Condition (ex. Healthy, Cancer, Time0)
#' \item BioReplicate : Unique ID for biological subject.
#' \item TechRepMixture : Unique ID for technical replicate of one TMT mixture.
#' \item Mixture : Unique ID for TMT mixture.
#' }
#'
#' @format A data frame with 100 rows and 8 variables.
#' @examples
#' head(quant.pd.msstats)
#'
"quant.pd.msstats"
#' Example of output from groupComparisonTMT function
#'
#' It is the output of groupComparisonTMT function,
#' which is the result of group comparions with the output of proteinSummarization function.
#' It should include the columns as below.
#' The variables are as follows:
#'
#' \itemize{
#' \item Protein : Protein ID
#' \item Label: Label of the pairwise comparision or contrast
#' \item log2FC: Log2 fold change
#' \item SE: Standard error of the comparsion of contrast results
#' \item DF: Degree of freedom
#' \item pvalue: Value of p statistic of the test
#' \item adj.pvalue: adjusted p value
#' \item issue: used for indicating the reason why a comparison is not testable. NA means the comparison is testable.
#' 'oneConditionMissing' means the protein has no measurements in one conndition of the comparison.
#' Furtherone, when 'issue = oneConditionMissing', 'log2FC = Inf' means the negative condition
#' (with coefficient -1 in the Label column) is missing and 'log2FC = -Inf' means
#' the positive condition (with coefficient 1 in the Label column) is missing.
#' completeMissing' means the protein has no measurements in all the connditions of the comparison.
#' unfittableModel' means there is no enough measurements to fit the linear model.
#' In other words, each condition has only one measurement.
#' }
#'
#' @format A data frame with 60 rows and 7 variables.
#' @examples
#' head(test.pairwise)
#'
"test.pairwise"
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