tableList {ppiData} | R Documentation

## A list of tables for the downloaded and parsed xml files from the IntAct database

### Description

This is a list of tables generated from the a script used to parse the xml files from the IntAct data repository.

tableList is a list that contains six data-frames (tables) that records all the various data given by IntAct. The names of these six tables are:

1. "acInfo" 2. "experimentInfo" 3. "ac2xref" 4. "interactionInfo" 5. "experiment2interaction" 6. "interaction2inteactor"

The "acInfo" data frame contains 4 columns: "ac", "type", "shortLabel", "fullName". They are IntAct accession numbers, types (experiment, interaction, or interactor), and short/long names, respectively. The reason to have the second column is because IntAct assigns an accession number to each experiment, interaction, and interactor. The second column is an indicator between these three. The accession numbers in the first column of this data frame are those accession numbers in the yeast xml files from the IntAct repository.

There are also 4 columns in the "experimentInfo" data frame: "ac","hostOrganism","interactionDetection", and "participantDetection". The IntAct accession numbers of experiments will be in the first column. The "hostOrganism" column is the tax id of the host organism (yeast in this case). The next two columns are the detection methods of the interaction and of the participant, respectively. The values in the 3rd and 4th columns are Proteomics Standards Initiative (PSI) Molecular Interaction (MI) identification codes. IntAct documents both the PSI MI 1.0 as well as PSI MI 2.5 codes.

The "ac2xref" data frame contains 4 columns: "ac", "db", "id", and "secondary". This data frame provides the cross references (among several databases) for each IntAct accession number. The column "ac" is the IntAct accession numbers, and the columns "db" and "id" are the reference database names and the corresponding identification code for that database. The secondary column provides secondary id if provided.

There are also 4 columns in the "interactionInfo" data frame: "ac", "interactionType", "confidenceUnit", and "confidenceValue". The first column contains all the interaction accession numbers among these xml files. The second column is the type of interaction. The values here are also the PSI MI codes. The third and forth columns are the confidence information for this interaction.

There are 2 columns in the "experiment2interaction" data frame: "experiment", and "interaction". This data frame tells us the what types of interactions were derived from the experiment. Both the experiments and the interactions are given by the IntAct accession numbers.

There are 3 columns in the "interaction2inteactor" data frame: "interaction", "interactor", and "role". The first column provide the type of interaction while the second column provides the interactors within the interaction. Both the "interaction" and the "interactor" are given by the IntAct accession numbers. The third column is the role (bait or prey) of the interactors.

### Usage

    data(tableList)

### Format

The format is: chr "tableList"

### Examples

    data(tableList)

[Package ppiData version 0.0.8 Index]