Query the contrast database with a set of contrasts

queryWithContrasts(
  contrasts,
  use = c("expressed.in.both", "all.genes"),
  exprThr = 0.25,
  organism = c("Human", "Mouse"),
  plotType = c("violin", "manh", "none"),
  detailTopn = 10,
  verbose = TRUE,
  BPPARAM = BiocParallel::bpparam(),
  chunk_size = 500,
  mode = c("ANALYSIS", "DEMO")
)

Arguments

contrasts: A SummarizedExperiment object with assays containing contrasts named INPUT_CONTRASTS, DECODED_CONTRASTS and RESIDUAL_CONTRASTS (at least one should be present) and context information in an assay named CONTEXT. The latter is only required when use="expressed.in.both". This is typically generated using decomposeVar.
use: Determines if all.genes or genes expressed in both query and target context will be used. Note that "expressed.in.both", though more accurate, is slower.
exprThr: is the quantile in the provided context that determines the expression value above which a gene is considered to be expressed. This same value is then used for thresholding the contrast database. Only applies when use="expressed.in.both".
organism: Uses the `orthosData` contrast database from this species. One of "Human" or "Mouse".
plotType: Select the type of visualization for the query results "violin", "manh" or "none" to suppress the plotting.
detailTopn: specifies the number of top hits for which metadata will be returned in the TopHits slot of the results.
verbose: Logical scalar indicating whether to print messages along the way.
BPPARAM: BiocParallelParam object specifying how parallelization is to be performed using e.g. MulticoreParam) or SnowParam).
chunk_size: Column dimension for the grid used to read blocks from the HDF5 Matrix. Sizes between 250 and 1000 are recommended. Smaller sizes reduce memory usage.
mode: When in "ANALYSIS" mode (default) the complete contrast DB is queried. "DEMO" mode employs a small "toy" database for the queries. "DEMO" should only be used for testing/demonstration purposes and never for actual analysis purposes.

Value

A list with three elements called "pearson.rhos", "zscores" and "TopHits", containing raw and z-scored Pearson's rho correlation coefficients between the query contrast(s) and the contrasts in the database, as well as detailed metadata for the detailTopn best hits.

Author

Panagiotis Papasaikas

Examples

MKL1_human <- readRDS(system.file("extdata", "GSE215150_MKL1_Human.rds",
package = "orthos"))

# Decompose contrasts:
dec_MKL1_human <- decomposeVar(M = MKL1_human, treatm = c(2, 3), cntr = c(1, 1), 
                               organism = "Human", verbose = FALSE)
#> see ?orthosData and browseVignettes('orthosData') for documentation
#> loading from cache
#> see ?orthosData and browseVignettes('orthosData') for documentation
#> loading from cache
#> see ?orthosData and browseVignettes('orthosData') for documentation
#> loading from cache

# Perform query against contrast DB with the decomposed fractions.
# !!!Note!!! mode="DEMO" for demonstration purposes only.                             
params <- BiocParallel::MulticoreParam(workers = 2)                              
query.res.human <- queryWithContrasts(dec_MKL1_human, organism = "Human", 
                                      BPPARAM = params, verbose = FALSE, 
                                      mode = "DEMO")
#> demo_decomposed_contrasts_human_rds  already present in cache at: /Users/runner/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
#> demo_decomposed_contrasts_human_hdf5  already present in cache at: /Users/runner/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5