Wrapper for CAMERA-PR

A wrapper for cameraPR.matrix that performs pre-ranked Correlation Adjusted MEan RAnk molecular signature analysis of differential analysis results.

Usage

run_cameraPR(
  DA_list = NULL,
  selected_omes = c("transcript-rna-seq", "prot-pr", "prot-ph", "prot-ol", "metab"),
  selected_tissues = "all",
  database = setdiff(names(MotrpacHumanPreSuspensionAnalysis::MOLECULAR_SIGNATURES),
    "PTMSIGDB"),
  path_to_gmt = NULL,
  min_size = 5L,
  overlap_cutoff = 0.7
)

Arguments

DA_list

list; a named list of data.frame objects, each containing differential analysis results for a specific tissue/assay combination. The list is nested, with tissues at the top level and omes within tissues, or already flattened with names of the form "tissue.assay". If NULL (default), the differential analysis results will be generated with load_differential_analysis. Unless wishing to analyze DA results that are not in MotrpacHumanPreSuspensionAnalysis, this should remain NULL.

selected_omes

character; one or more character strings selected from the following options: "transcript-rna-seq", "prot-pr", "prot-ph", and "metab" (all metabolomics platforms). Passed to load_differential_analysis.

selected_tissues

character; passed to load_differential_analysis. One or more of the following: "all", "muscle", "adipose", or "blood".

database

character; one or more names specifying the database(s) to test. Options are (case insensitive) "BIOCARTA", "KEGG_MEDICUS", "PID", "REACTOME", "WP" (WikiPathways database), "GOBP", "GOCC", "GOMF", "MITOCARTA" (MitoCarta3.0 database), "PSP" (PhosphoSitePlus kinases; only valid when selected_omes contains "prot-ph"), or "REFMET" (RefMet chemical subclasses; only valid when selected_omes contains "metab"). See MOLECULAR_SIGNATURES for details.

path_to_gmt

character; (optional) path to one or more GMT files. Passed to TMSig::readGMT. If provided, database is ignored.

min_size

integer; the minimum set size for testing.

overlap_cutoff

numeric; the minimum proportion of genes in each set that must appear in a given dataset. Used to pre-filter sets. Does not affect "metab" or "prot-ph" results. This will always be 0.1 for "prot-ol" results.

Value

An object of class data.frame with the following columns:

tissue

factor; the tissue.

html

\item{\code{assay}}{factor; the omics assay.} \item{\code{contrast_type}}{factor; the type of contrast.} \item{\code{contrast}}{factor; the contrast of interest.} \item{\code{contrast_short}}{factor; shortened contrasts.} \item{\code{collection}}{factor; the broad molecular signature collection. Only included when \code{path_to_gmt} is \code{NULL}. See \code{\link[MotrpacHumanPreSuspensionAnalysis]{SET_TO_ID}} for details.} \item{\code{database}}{factor; the molecular signature database. Only included when \code{path_to_gmt} is \code{NULL}. See \code{\link[MotrpacHumanPreSuspensionAnalysis]{SET_TO_ID}} for details.} \item{\code{set_id}}{character; a unique ID for the molecular signature. See \code{\link[MotrpacHumanPreSuspensionAnalysis]{SET_TO_ID}} for details.} \item{\code{set}}{character; the molecular signature being tested. For global proteomics and transcriptomics, these are gene sets. For phosphoproteomics, these are kinase sets.} \item{\code{set_short}}{character; a shortened version of \code{set}. Only included when \code{path_to_gmt} is \code{NULL}. See \code{\link[MotrpacHumanPreSuspensionAnalysis]{SET_TO_ID}} for details.} \item{\code{set_size}}{integer; the number of molecules in the set that were present in the DA results for that specific tissue/assay combination.} \item{\code{set_size_DB}}{integer; the number of molecules in the set, as defined in the GMT file.} \item{\code{size_ratio}}{numeric; the ratio of \code{set_size} to \code{set_size_DB}, rounded to the nearest thousandth. A measure of confidence that the gene set being tested is correctly described by the entry in the \code{set} column. While smaller values do not necessarily indicate that the results are unreliable, terms from the gene set databases should be treated with caution.} \item{\code{direction}}{factor; the direction of change: \code{"Up"} or \code{"Down"}.} \item{\code{t}}{numeric; the two-sample t-statistic.} \item{\code{df}}{integer; the available degrees of freedom.} \item{\code{z.std}}{numeric; standard Normal equivalents of \code{t}.} \item{\code{p_value}}{numeric; the two-sided p-value.} \item{\code{adj_p_value}}{numeric; the BH-adjusted p-value. P-values are adjusted within each combination of tissue, assay, contrast, and collection.} html

See also

MOLECULAR_SIGNATURES, SET_TO_ID

Author

Tyler Sagendorf

Examples

if (FALSE) { # \dontrun{
# Test Reactome and Gene Ontology Biological Processes
# databases on muscle global proteomics.
x1 <- run_cameraPR(selected_omes = "prot-pr",
                   selected_tissues = "muscle",
                   database = c("GOBP", "REACTOME"))

# Test all omes using all molecular signature databases
x2 <- run_cameraPR()
} # }