fragpipe_annotation: Example annotation file for a TMT FragPipe experiment.
In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications
fragpipe_annotation R Documentation
Example annotation file for a TMT FragPipe experiment.
Description
Automatically created by FragPipe, manually checked by the user and input
into the FragPipetoMSstatsPTMFormat 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
fragpipe_annotation
Format
A data.table with 7 columns.
Details
Run : Run name that matches exactly with FragPipe run. Used to join
evidence and metadata in annotation file.
Fraction : If multiple fractions were used (i.e. the same mixture
split into multiple fractions) enter that here.
TechRepMixture : Multiple runs using the same bioreplicate
Channel : Mixture channel used
Condition : Name of condition that was used for each run.
Mixture : The unique mixture (plex) name
BioReplicate : Name of biological replicate. Repeating the same name
here will tell MSstatsPTM that the experiment is a repeated measure design.
Examples
head(fragpipe_annotation)
Vitek-Lab/MSstatsPTM documentation built on Dec. 19, 2024, 6:02 a.m.
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| fragpipe_annotation | R Documentation |
Example annotation file for a TMT FragPipe experiment.
Description
Automatically created by FragPipe, manually checked by the user and input into the FragPipetoMSstatsPTMFormat 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
fragpipe_annotation
Format
A data.table with 7 columns.
Details
Run : Run name that matches exactly with FragPipe run. Used to join evidence and metadata in annotation file.
Fraction : If multiple fractions were used (i.e. the same mixture split into multiple fractions) enter that here. TechRepMixture : Multiple runs using the same bioreplicate
Channel : Mixture channel used
Condition : Name of condition that was used for each run.
Mixture : The unique mixture (plex) name
BioReplicate : Name of biological replicate. Repeating the same name here will tell MSstatsPTM that the experiment is a repeated measure design.
Examples
head(fragpipe_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.
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