Omics integration¶

MATLAB functions in RAVEN/omics of the RAVEN toolbox. Help text is collected from the source of the tracked branch.

Functions¶

Function	Summary
`parseHPA`	Parse a database dump of the Human Protein Atlas (HPA).
`parseHPArna`	Parse a dump of Human Protein Atlas (HPA) RNA-Seq data.
`scoreModel`	Score model reactions and genes from HPA and/or array data.

Reference¶

parseHPA¶

Parse a database dump of the Human Protein Atlas (HPA).

Input arguments:

Name	Type	Description	Default
`fileName`	`char`	comma- or tab-separated database dump of HPA protein data. For details regarding the format, see http://www.proteinatlas.org/about/download.	required

Name-value arguments:

Name	Type	Description	Default
`version`	`double`	accepted for backward compatibility but ignored; the format is now inferred from the column headers (default 19).

Output arguments:

Name	Type	Description
`hpaData`	`struct`	parsed HPA data with fields: genes : cell array with the unique gene IDs (Ensembl in v>=18) geneNames : cell array with the gene symbols (present in v>=18 only) tissues : cell array with the tissue names (may not be unique; one entry per tissue-cell-type combination) celltypes : cell array with the cell type names for each tissue levels : cell array with the unique expression level labels types : cell array with the unique evidence types (v<18 only) reliabilities : cell array with the unique reliability levels gene2Level : sparse gene × tissue-cell-type matrix; value i,j is the index in hpaData.levels for gene i in tissue-cell-type j gene2Type : sparse gene × tissue-cell-type matrix (v<18 only) gene2Reliability : sparse gene × tissue-cell-type matrix; value i,j is the index in hpaData.reliabilities for gene i in tissue-cell-type j

Examples:

hpaData = parseHPA(fileName);

parseHPArna¶

Parse a dump of Human Protein Atlas (HPA) RNA-Seq data.

Input arguments:

Name	Type	Description	Default
`fileName`	`char`	tab-separated database dump of HPA RNA data. For details regarding the format, see http://www.proteinatlas.org/about/download.	required

Name-value arguments:

Name	Type	Description	Default
`version`	`double`	accepted for backward compatibility but ignored; the format is now inferred from the column headers (default 19).

Output arguments:

Name	Type	Description
`arrayData`	`struct`	parsed HPA RNA data with fields: genes : cell array with the unique Ensembl gene IDs geneNames : cell array with the gene symbols tissues : cell array with the unique tissue (or sample) names levels : matrix of expression values (rows = genes, cols = tissues)

Examples:

arrayData = parseHPArna(fileName);

scoreModel¶

Score model reactions and genes from HPA and/or array data.

Scores the reactions and genes in a model based on expression data from HPA and/or gene arrays.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	a model structure.	required
`hpaData`	`struct`	HPA data structure from parseHPA (optional if arrayData is supplied, default []).	required

Name-value arguments:

Name	Type	Description
`arrayData`	`struct`	gene expression data structure (optional if hpaData is supplied, default []) with fields: genes : cell array with the unique gene names tissues : cell array with the tissue names. The list may not be unique, as there can be multiple cell types per tissue celltypes : cell array with the cell type names for each tissue levels : GENESxTISSUES array with the expression level for each gene in each tissue/celltype. NaN should be used when no measurement was performed threshold : a single value or a vector of gene expression thresholds, above which genes are considered to be "expressed". (optional, by default, the mean expression levels of each gene across all tissues in arrayData will be used as the threshold values)
`tissue`	`char`	tissue to score for. Should exist in either hpaData.tissues or arrayData.tissues.
`celltype`	`char`	cell type to score for. Should exist in either hpaData.celltypes or arrayData.celltypes for this tissue (default is to use the best values among all the cell types for the tissue). Use [] if you want to supply more arguments.
`noGeneScore`	`double`	score for reactions without genes (default -2).
`multipleGeneScoring`	`char`	determines how scores are calculated for reactions with several genes, "best" or "average" (default "best").
`multipleCellScoring`	`char`	determines how scores are calculated when several cell types are used, "best" or "average" (default "best").
`hpaLevelScores`	`struct`	structure with numerical scores for the expression level categories from HPA. The structure should have a "names" and a "scores" field (default see code for default scores).

Output arguments:

Name	Type	Description
`rxnScores`	`double`	scores for each of the reactions in model.
`geneScores`	`double`	scores for each of the genes in model. Genes which are not in the dataset(s) have -Inf as scores.
`hpaScores`	`double`	scores for each of the genes in model if only taking hpaData into account. Genes which are not in the dataset(s) have -Inf as scores.
`arrayScores`	`double`	scores for each of the genes in model if only taking arrayData into account. Genes which are not in the dataset(s) have -Inf as scores.

Examples:

[rxnScores, geneScores, hpaScores, arrayScores] = scoreModel(model, ...
    hpaData, arrayData, tissue, celltype, noGeneScore, ...
    multipleGeneScoring, multipleCellScoring, hpaLevelScores);