Nothing
R/data.R
In scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
##' @title Example MaxQuant/SCoPE2 output
##'
##' @description
##'
##' A `data.frame` with 1088 observations and 139 variables, as
##' produced by reading a MaxQuant output file with
##' [read.delim()].
##'
##' - Sequence: a character vector
##' - Length: a numeric vector
##' - Modifications: a character vector
##' - Modified.sequence: a character vector
##' - Deamidation..N..Probabilities: a character vector
##' - Oxidation..M..Probabilities: a character vector
##' - Deamidation..N..Score.Diffs: a character vector
##' - Oxidation..M..Score.Diffs: a character vector
##' - Acetyl..Protein.N.term.: a numeric vector
##' - Deamidation..N.: a numeric vector
##' - Oxidation..M.: a numeric vector
##' - Missed.cleavages: a numeric vector
##' - Proteins: a character vector
##' - Leading.proteins: a character vector
##' - protein: a character vector
##' - Gene.names: a character vector
##' - Protein.names: a character vector
##' - Type: a character vector
##' - Set: a character vector
##' - MS.MS.m.z: a numeric vector
##' - Charge: a numeric vector
##' - m.z: a numeric vector
##' - Mass: a numeric vector
##' - Resolution: a numeric vector
##' - Uncalibrated...Calibrated.m.z..ppm.: a numeric vector
##' - Uncalibrated...Calibrated.m.z..Da.: a numeric vector
##' - Mass.error..ppm.: a numeric vector
##' - Mass.error..Da.: a numeric vector
##' - Uncalibrated.mass.error..ppm.: a numeric vector
##' - Uncalibrated.mass.error..Da.: a numeric vector
##' - Max.intensity.m.z.0: a numeric vector
##' - Retention.time: a numeric vector
##' - Retention.length: a numeric vector
##' - Calibrated.retention.time: a numeric vector
##' - Calibrated.retention.time.start: a numeric vector
##' - Calibrated.retention.time.finish: a numeric vector
##' - Retention.time.calibration: a numeric vector
##' - Match.time.difference: a logical vector
##' - Match.m.z.difference: a logical vector
##' - Match.q.value: a logical vector
##' - Match.score: a logical vector
##' - Number.of.data.points: a numeric vector
##' - Number.of.scans: a numeric vector
##' - Number.of.isotopic.peaks: a numeric vector
##' - PIF: a numeric vector
##' - Fraction.of.total.spectrum: a numeric vector
##' - Base.peak.fraction: a numeric vector
##' - PEP: a numeric vector
##' - MS.MS.count: a numeric vector
##' - MS.MS.scan.number: a numeric vector
##' - Score: a numeric vector
##' - Delta.score: a numeric vector
##' - Combinatorics: a numeric vector
##' - Intensity: a numeric vector
##' - Reporter.intensity.corrected.0: a numeric vector
##' - Reporter.intensity.corrected.1: a numeric vector
##' - Reporter.intensity.corrected.2: a numeric vector
##' - Reporter.intensity.corrected.3: a numeric vector
##' - Reporter.intensity.corrected.4: a numeric vector
##' - Reporter.intensity.corrected.5: a numeric vector
##' - Reporter.intensity.corrected.6: a numeric vector
##' - Reporter.intensity.corrected.7: a numeric vector
##' - Reporter.intensity.corrected.8: a numeric vector
##' - Reporter.intensity.corrected.9: a numeric vector
##' - Reporter.intensity.corrected.10: a numeric vector
##' - RI1: a numeric vector
##' - RI2: a numeric vector
##' - RI3: a numeric vector
##' - RI4: a numeric vector
##' - RI5: a numeric vector
##' - RI6: a numeric vector
##' - RI7: a numeric vector
##' - RI8: a numeric vector
##' - RI9: a numeric vector
##' - RI10: a numeric vector
##' - RI11: a numeric vector
##' - Reporter.intensity.count.0: a numeric vector
##' - Reporter.intensity.count.1: a numeric vector
##' - Reporter.intensity.count.2: a numeric vector
##' - Reporter.intensity.count.3: a numeric vector
##' - Reporter.intensity.count.4: a numeric vector
##' - Reporter.intensity.count.5: a numeric vector
##' - Reporter.intensity.count.6: a numeric vector
##' - Reporter.intensity.count.7: a numeric vector
##' - Reporter.intensity.count.8: a numeric vector
##' - Reporter.intensity.count.9: a numeric vector
##' - Reporter.intensity.count.10: a numeric vector
##' - Reporter.PIF: a logical vector
##' - Reporter.fraction: a logical vector
##' - Reverse: a character vector
##' - Potential.contaminant: a logical vector
##' - id: a numeric vector
##' - Protein.group.IDs: a character vector
##' - Peptide.ID: a numeric vector
##' - Mod..peptide.ID: a numeric vector
##' - MS.MS.IDs: a character vector
##' - Best.MS.MS: a numeric vector
##' - AIF.MS.MS.IDs: a logical vector
##' - Deamidation..N..site.IDs: a numeric vector
##' - Oxidation..M..site.IDs: a logical vector
##' - remove: a logical vector
##' - dart_PEP: a numeric vector
##' - dart_qval: a numeric vector
##' - razor_protein_fdr: a numeric vector
##' - Deamidation..NQ..Probabilities: a logical vector
##' - Deamidation..NQ..Score.Diffs: a logical vector
##' - Deamidation..NQ.: a logical vector
##' - Reporter.intensity.corrected.11: a logical vector
##' - Reporter.intensity.corrected.12: a logical vector
##' - Reporter.intensity.corrected.13: a logical vector
##' - Reporter.intensity.corrected.14: a logical vector
##' - Reporter.intensity.corrected.15: a logical vector
##' - Reporter.intensity.corrected.16: a logical vector
##' - RI12: a logical vector
##' - RI13: a logical vector
##' - RI14: a logical vector
##' - RI15: a logical vector
##' - RI16: a logical vector
##' - Reporter.intensity.count.11: a logical vector
##' - Reporter.intensity.count.12: a logical vector
##' - Reporter.intensity.count.13: a logical vector
##' - Reporter.intensity.count.14: a logical vector
##' - Reporter.intensity.count.15: a logical vector
##' - Reporter.intensity.count.16: a logical vector
##' - Deamidation..NQ..site.IDs: a logical vector
##' - input_id: a logical vector
##' - rt_minus: a logical vector
##' - rt_plus: a logical vector
##' - mu: a logical vector
##' - muij: a logical vector
##' - sigmaij: a logical vector
##' - pep_new: a logical vector
##' - exp_id: a logical vector
##' - peptide_id: a logical vector
##' - stan_peptide_id: a logical vector
##' - exclude: a logical vector
##' - residual: a logical vector
##' - participated: a logical vector
##' - peptide: a character vector
##'
##' @usage data("mqScpData")
##'
##' @details
##'
##' The dataset is a subset of the SCoPE2 dataset (version 2, Specht
##' et al. 2019,
##' [BioRXiv](https://www.biorxiv.org/content/10.1101/665307v3)). The
##' input file `evidence_unfiltered.csv` was downloaded from a
##' [Google Drive repository](https://drive.google.com/drive/folders/1VzBfmNxziRYqayx3SP-cOe2gu129Obgx).
##' The MaxQuant evidence file was loaded and the data was cleaned
##' (renaming columns, removing duplicate fields,...). MS runs that
##' were selected in the `scp1` dataset (see `?scp1`) were kept along
##' with a blank run. The data is stored as a `data.frame`.
##'
##' @seealso [readSCP()] for an example on how `mqScpData` is
##' parsed into a [QFeatures] object.
##'
##' @md
"mqScpData"
##' @title Single cell sample annotation
##'
##' @description
##'
##' A data frame with 48 observations on the following 6 variables.
##' - Set: a character vector
##' - Channel: a character vector
##' - SampleType: a character vector
##' - lcbatch: a character vector
##' - sortday: a character vector
##' - digest: a character vector
##'
##' @usage data("sampleAnnotation")
##'
##' @details
##'
##' ##' The dataset is a subset of the SCoPE2 dataset (version 2, Specht
##' et al. 2019,
##' [BioRXiv](https://www.biorxiv.org/content/10.1101/665307v3)). The
##' input files `batch.csv` and `annotation.csv` were downloaded from a
##' [Google Drive repository](https://drive.google.com/drive/folders/1VzBfmNxziRYqayx3SP-cOe2gu129Obgx).
##' The two files were loaded and the columns names were adapted for
##' consistency with `mqScpData` table (see `?mqScpData`). The two
##' tables were filtered to contain only sets present in ``mqScpData`.
##' The tables were then merged based on the run ID, hence merging the
##' sample annotation and the batch annotation. Finally, annotation
##' for the blank run was added manually. The data is stored as a
##' `data.frame`.
##'
##' @seealso [readSCP()] to see how this file is used.
##'
##' @md
"sampleAnnotation"
##' @title Single Cell QFeatures data
##'
##' @description
##'
##' A small [QFeatures] object with SCoPE2 data. The object is
##' composed of 5 assays, including 3 PSM-level assays, 1 peptide
##' assay and 1 protein assay.
##'
##' @usage data("scp1")
##'
##' @details
##'
##' The dataset is a subset of the SCoPE2 dataset (version 2, Specht
##' et al. 2019,
##' [BioRXiv](https://www.biorxiv.org/content/10.1101/665307v3)).
##' This dataset was converted to a [`QFeatures`] object where each
##' assay in stored as a [`SingleCellExperiment`] object. One assay
##' per chromatographic batch ("LCA9", "LCA10", "LCB3") was randomly
##' sampled. For each assay, 100 proteins were randomly sampled. PSMs
##' were then aggregated to peptides and joined in a single assay.
##' Then peptides were aggregated to proteins.
##'
##' @md
##'
##' @docType data
##'
##' @examples
##' data("scp1")
##' scp1
"scp1"
Try the scp package in your browser
Any scripts or data that you put into this service are public.
scp documentation built on Nov. 8, 2020, 8:20 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
##' @title Example MaxQuant/SCoPE2 output
##'
##' @description
##'
##' A `data.frame` with 1088 observations and 139 variables, as
##' produced by reading a MaxQuant output file with
##' [read.delim()].
##'
##' - Sequence: a character vector
##' - Length: a numeric vector
##' - Modifications: a character vector
##' - Modified.sequence: a character vector
##' - Deamidation..N..Probabilities: a character vector
##' - Oxidation..M..Probabilities: a character vector
##' - Deamidation..N..Score.Diffs: a character vector
##' - Oxidation..M..Score.Diffs: a character vector
##' - Acetyl..Protein.N.term.: a numeric vector
##' - Deamidation..N.: a numeric vector
##' - Oxidation..M.: a numeric vector
##' - Missed.cleavages: a numeric vector
##' - Proteins: a character vector
##' - Leading.proteins: a character vector
##' - protein: a character vector
##' - Gene.names: a character vector
##' - Protein.names: a character vector
##' - Type: a character vector
##' - Set: a character vector
##' - MS.MS.m.z: a numeric vector
##' - Charge: a numeric vector
##' - m.z: a numeric vector
##' - Mass: a numeric vector
##' - Resolution: a numeric vector
##' - Uncalibrated...Calibrated.m.z..ppm.: a numeric vector
##' - Uncalibrated...Calibrated.m.z..Da.: a numeric vector
##' - Mass.error..ppm.: a numeric vector
##' - Mass.error..Da.: a numeric vector
##' - Uncalibrated.mass.error..ppm.: a numeric vector
##' - Uncalibrated.mass.error..Da.: a numeric vector
##' - Max.intensity.m.z.0: a numeric vector
##' - Retention.time: a numeric vector
##' - Retention.length: a numeric vector
##' - Calibrated.retention.time: a numeric vector
##' - Calibrated.retention.time.start: a numeric vector
##' - Calibrated.retention.time.finish: a numeric vector
##' - Retention.time.calibration: a numeric vector
##' - Match.time.difference: a logical vector
##' - Match.m.z.difference: a logical vector
##' - Match.q.value: a logical vector
##' - Match.score: a logical vector
##' - Number.of.data.points: a numeric vector
##' - Number.of.scans: a numeric vector
##' - Number.of.isotopic.peaks: a numeric vector
##' - PIF: a numeric vector
##' - Fraction.of.total.spectrum: a numeric vector
##' - Base.peak.fraction: a numeric vector
##' - PEP: a numeric vector
##' - MS.MS.count: a numeric vector
##' - MS.MS.scan.number: a numeric vector
##' - Score: a numeric vector
##' - Delta.score: a numeric vector
##' - Combinatorics: a numeric vector
##' - Intensity: a numeric vector
##' - Reporter.intensity.corrected.0: a numeric vector
##' - Reporter.intensity.corrected.1: a numeric vector
##' - Reporter.intensity.corrected.2: a numeric vector
##' - Reporter.intensity.corrected.3: a numeric vector
##' - Reporter.intensity.corrected.4: a numeric vector
##' - Reporter.intensity.corrected.5: a numeric vector
##' - Reporter.intensity.corrected.6: a numeric vector
##' - Reporter.intensity.corrected.7: a numeric vector
##' - Reporter.intensity.corrected.8: a numeric vector
##' - Reporter.intensity.corrected.9: a numeric vector
##' - Reporter.intensity.corrected.10: a numeric vector
##' - RI1: a numeric vector
##' - RI2: a numeric vector
##' - RI3: a numeric vector
##' - RI4: a numeric vector
##' - RI5: a numeric vector
##' - RI6: a numeric vector
##' - RI7: a numeric vector
##' - RI8: a numeric vector
##' - RI9: a numeric vector
##' - RI10: a numeric vector
##' - RI11: a numeric vector
##' - Reporter.intensity.count.0: a numeric vector
##' - Reporter.intensity.count.1: a numeric vector
##' - Reporter.intensity.count.2: a numeric vector
##' - Reporter.intensity.count.3: a numeric vector
##' - Reporter.intensity.count.4: a numeric vector
##' - Reporter.intensity.count.5: a numeric vector
##' - Reporter.intensity.count.6: a numeric vector
##' - Reporter.intensity.count.7: a numeric vector
##' - Reporter.intensity.count.8: a numeric vector
##' - Reporter.intensity.count.9: a numeric vector
##' - Reporter.intensity.count.10: a numeric vector
##' - Reporter.PIF: a logical vector
##' - Reporter.fraction: a logical vector
##' - Reverse: a character vector
##' - Potential.contaminant: a logical vector
##' - id: a numeric vector
##' - Protein.group.IDs: a character vector
##' - Peptide.ID: a numeric vector
##' - Mod..peptide.ID: a numeric vector
##' - MS.MS.IDs: a character vector
##' - Best.MS.MS: a numeric vector
##' - AIF.MS.MS.IDs: a logical vector
##' - Deamidation..N..site.IDs: a numeric vector
##' - Oxidation..M..site.IDs: a logical vector
##' - remove: a logical vector
##' - dart_PEP: a numeric vector
##' - dart_qval: a numeric vector
##' - razor_protein_fdr: a numeric vector
##' - Deamidation..NQ..Probabilities: a logical vector
##' - Deamidation..NQ..Score.Diffs: a logical vector
##' - Deamidation..NQ.: a logical vector
##' - Reporter.intensity.corrected.11: a logical vector
##' - Reporter.intensity.corrected.12: a logical vector
##' - Reporter.intensity.corrected.13: a logical vector
##' - Reporter.intensity.corrected.14: a logical vector
##' - Reporter.intensity.corrected.15: a logical vector
##' - Reporter.intensity.corrected.16: a logical vector
##' - RI12: a logical vector
##' - RI13: a logical vector
##' - RI14: a logical vector
##' - RI15: a logical vector
##' - RI16: a logical vector
##' - Reporter.intensity.count.11: a logical vector
##' - Reporter.intensity.count.12: a logical vector
##' - Reporter.intensity.count.13: a logical vector
##' - Reporter.intensity.count.14: a logical vector
##' - Reporter.intensity.count.15: a logical vector
##' - Reporter.intensity.count.16: a logical vector
##' - Deamidation..NQ..site.IDs: a logical vector
##' - input_id: a logical vector
##' - rt_minus: a logical vector
##' - rt_plus: a logical vector
##' - mu: a logical vector
##' - muij: a logical vector
##' - sigmaij: a logical vector
##' - pep_new: a logical vector
##' - exp_id: a logical vector
##' - peptide_id: a logical vector
##' - stan_peptide_id: a logical vector
##' - exclude: a logical vector
##' - residual: a logical vector
##' - participated: a logical vector
##' - peptide: a character vector
##'
##' @usage data("mqScpData")
##'
##' @details
##'
##' The dataset is a subset of the SCoPE2 dataset (version 2, Specht
##' et al. 2019,
##' [BioRXiv](https://www.biorxiv.org/content/10.1101/665307v3)). The
##' input file `evidence_unfiltered.csv` was downloaded from a
##' [Google Drive repository](https://drive.google.com/drive/folders/1VzBfmNxziRYqayx3SP-cOe2gu129Obgx).
##' The MaxQuant evidence file was loaded and the data was cleaned
##' (renaming columns, removing duplicate fields,...). MS runs that
##' were selected in the `scp1` dataset (see `?scp1`) were kept along
##' with a blank run. The data is stored as a `data.frame`.
##'
##' @seealso [readSCP()] for an example on how `mqScpData` is
##' parsed into a [QFeatures] object.
##'
##' @md
"mqScpData"
##' @title Single cell sample annotation
##'
##' @description
##'
##' A data frame with 48 observations on the following 6 variables.
##' - Set: a character vector
##' - Channel: a character vector
##' - SampleType: a character vector
##' - lcbatch: a character vector
##' - sortday: a character vector
##' - digest: a character vector
##'
##' @usage data("sampleAnnotation")
##'
##' @details
##'
##' ##' The dataset is a subset of the SCoPE2 dataset (version 2, Specht
##' et al. 2019,
##' [BioRXiv](https://www.biorxiv.org/content/10.1101/665307v3)). The
##' input files `batch.csv` and `annotation.csv` were downloaded from a
##' [Google Drive repository](https://drive.google.com/drive/folders/1VzBfmNxziRYqayx3SP-cOe2gu129Obgx).
##' The two files were loaded and the columns names were adapted for
##' consistency with `mqScpData` table (see `?mqScpData`). The two
##' tables were filtered to contain only sets present in ``mqScpData`.
##' The tables were then merged based on the run ID, hence merging the
##' sample annotation and the batch annotation. Finally, annotation
##' for the blank run was added manually. The data is stored as a
##' `data.frame`.
##'
##' @seealso [readSCP()] to see how this file is used.
##'
##' @md
"sampleAnnotation"
##' @title Single Cell QFeatures data
##'
##' @description
##'
##' A small [QFeatures] object with SCoPE2 data. The object is
##' composed of 5 assays, including 3 PSM-level assays, 1 peptide
##' assay and 1 protein assay.
##'
##' @usage data("scp1")
##'
##' @details
##'
##' The dataset is a subset of the SCoPE2 dataset (version 2, Specht
##' et al. 2019,
##' [BioRXiv](https://www.biorxiv.org/content/10.1101/665307v3)).
##' This dataset was converted to a [`QFeatures`] object where each
##' assay in stored as a [`SingleCellExperiment`] object. One assay
##' per chromatographic batch ("LCA9", "LCA10", "LCB3") was randomly
##' sampled. For each assay, 100 proteins were randomly sampled. PSMs
##' were then aggregated to peptides and joined in a single assay.
##' Then peptides were aggregated to proteins.
##'
##' @md
##'
##' @docType data
##'
##' @examples
##' data("scp1")
##' scp1
"scp1"
Try the scp package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.