cptac: CPTAC data
In UCLouvain-CBIO/rWSBIM1322: Companion Package for WSBIM1322 Course
cptac_se R Documentation
CPTAC data
Description
The data stems from the 6th study of the Clinical Proteomic
Technology Assessment for Cancer (CPTAC). The authors spiked the
Sigma Universal Protein Standard mixture 1 (UPS1) containing 48
different human proteins in a protein background of 60 ng/microL
Saccharomyces cerevisiae strain BY4741. Two different spike-in
concentrations were used: 6A (0.25 fmol UPS1 proteins/microL) and
6B (0.74 fmol UPS1 proteins/microL). In this subset, we limited
ourselves to the data of LTQ-Orbitrap W at site 56. The data were
searched with MaxQuant version 1.5.2.8, and detailed search
settings were described in Goeminne et al. (2016). Three replicates
peptide quantitation data are available for each concentration.
Usage
cptac_se
Format
An object of class SummarizedExperiment with 4051 rows and 6 columns.
Details
The data are available as SummarizedExperiment objects.
See the proteomics tutorial from the Bioinformatics Summer School
2019 (https://lgatto.github.io/bioc-ms-prot/bss-lab.html) for
scripts on how these data were processed.
Examples
library("SummarizedExperiment")
data(cptac_se)
cptac_se
data(cptac_se_prot)
cptac_se_prot
UCLouvain-CBIO/rWSBIM1322 documentation built on Nov. 28, 2022, 11:43 a.m.
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| cptac_se | R Documentation |
CPTAC data
Description
The data stems from the 6th study of the Clinical Proteomic Technology Assessment for Cancer (CPTAC). The authors spiked the Sigma Universal Protein Standard mixture 1 (UPS1) containing 48 different human proteins in a protein background of 60 ng/microL Saccharomyces cerevisiae strain BY4741. Two different spike-in concentrations were used: 6A (0.25 fmol UPS1 proteins/microL) and 6B (0.74 fmol UPS1 proteins/microL). In this subset, we limited ourselves to the data of LTQ-Orbitrap W at site 56. The data were searched with MaxQuant version 1.5.2.8, and detailed search settings were described in Goeminne et al. (2016). Three replicates peptide quantitation data are available for each concentration.
Usage
cptac_se
Format
An object of class SummarizedExperiment with 4051 rows and 6 columns.
Details
The data are available as SummarizedExperiment objects.
See the proteomics tutorial from the Bioinformatics Summer School 2019 (https://lgatto.github.io/bioc-ms-prot/bss-lab.html) for scripts on how these data were processed.
Examples
library("SummarizedExperiment")
data(cptac_se)
cptac_se
data(cptac_se_prot)
cptac_se_prot
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.
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