maxq_lf_annotation: Example annotation file for a label-free MaxQuant experiment.
In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications
maxq_lf_annotation R Documentation
Example annotation file for a label-free MaxQuant experiment.
Description
Must be manually created by the user and input into the
MaxQtoMSstatsPTMFormat converter. Requires the correct columns and maps the
experimental desing into the MSstats format. Specify unique bioreplicates for
group comparison designs, and the same bioreplicate for repeated measure
designs. The columns and descriptions are below.
Usage
maxq_lf_annotation
Format
A data.table with 5 columns.
Details
Run : Run name that matches exactly with MaxQuant run. Used to join
evidence and metadata in annotation file.
Condition : Name of condition that was used for each run.
BioReplicate : Name of biological replicate. Repeating the same name
here will tell MSstatsPTM that the experiment is a repeated measure design.
Raw.file : Run name that matches exactly with MaxQuant run. Used to join
evidence and metadata in annotation file.
IsotopeLabelType: Name of isotope label. May be all L or unique
depending on experimental design.
Examples
head(maxq_lf_annotation)
Vitek-Lab/MSstatsPTM documentation built on Dec. 19, 2024, 6:02 a.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.
| maxq_lf_annotation | R Documentation |
Example annotation file for a label-free MaxQuant experiment.
Description
Must be manually created by the user and input into the MaxQtoMSstatsPTMFormat converter. Requires the correct columns and maps the experimental desing into the MSstats format. Specify unique bioreplicates for group comparison designs, and the same bioreplicate for repeated measure designs. The columns and descriptions are below.
Usage
maxq_lf_annotation
Format
A data.table with 5 columns.
Details
Run : Run name that matches exactly with MaxQuant run. Used to join evidence and metadata in annotation file.
Condition : Name of condition that was used for each run.
BioReplicate : Name of biological replicate. Repeating the same name here will tell MSstatsPTM that the experiment is a repeated measure design.
Raw.file : Run name that matches exactly with MaxQuant run. Used to join evidence and metadata in annotation file.
IsotopeLabelType: Name of isotope label. May be all
Lor unique depending on experimental design.
Examples
head(maxq_lf_annotation)
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.