props: PRObabilistic Pathway Scores (PROPS)

In PROPS: PRObabilistic Pathway Score (PROPS)

Description

Calculates PRObabilistic Pathway Scores (PROPS), which are pathway-based features, from gene-based data.

Usage

props(healthy_dat, dat, pathway_edges = NULL, batch_correct = FALSE, healthy_batches = NULL, dat_batches = NULL)

Arguments

healthy_dat	Data frame or ExpressionSet of healthy data used to parameterize the pathways. Healthy data frame should be formatted as one sample per row, and columns should correspond to genes and be named by the gene Entrez ID. If using ExpressionSet, map row.names probes to corresponding Entrez IDs before proceeding.
dat	Data frame or ExpressionSet of patient data for which to calculate pathway-based scores. Data frame should be formatted as one sample per row, and columns should correspond to genes and be named by the gene Entrez ID. If using ExpressionSet, map row.names probes to corresponding Entrez IDs before proceeding.
pathway_edges	Optional user specified pathway edges. If no pathway edges are provided, KEGG pathways are used by default. User input edges should be a data frame with 3 columns, where columns 1 and 2 are the source (from) and sink (to) of the edge, and column 3 is the pathway ID or name the edge belongs to. Genes should be named by Entrez ID.
batch_correct	Optional flag to do batch correction using ComBat. If TRUE, then batch numbers must be provided.
healthy_batches	Batch covariate numbers, as a numeric vector, corresponding to the healthy data. For example, given 5 healthy patients from two batches, an example input would be (1, 2, 2, 1, 1).
dat_batches	Batch covariate numbers, as a numeric vector, corresponding to the patient data. For example, given 10 patients from three batches, an example input would be (1, 3, 2, 1, 3, 3, 2, 1, 2, 1). Batch "1" is the same for healthy data and patient data, indicating in this example there are 3 healthy samples and 4 patient samples from the same batch.

Value

Returns a data frame of pathway-based log-likelihood values, where each row corresponds to a pathway. The first two columns are the KEGG pathway ID and name, and the remaining columns correspond to each sample's pathway features.

Author(s)

Lichy Han

References

Lichy Han, Mateusz Maciejewski, Christoph Brockel, William Gordon, Scott B. Snapper, Joshua R. Korzenik, Lovisa Afzelius, Russ B. Altman. A PRObabilistic Pathway Score (PROPS) for Classification with Applications to Inflammatory Bowel Disease.

Examples

#Load in randomly generated example data
#Each row is a sample
#Each column is a gene, named with Entrez Gene ID
data(example_healthy)
data(example_data)

#Run PROPS with default KEGG pathway edges
props_features <- props(example_healthy, example_data)

#Run PROPS with user input edges
data(example_edges)
props_features2 <- props(example_healthy, example_data, example_edges)

PROPS documentation built on Nov. 8, 2020, 8:03 p.m.