scMappR (version 1.0.11)

DeconRNAseq_CRAN: DeconRNASeq CRAN compatible

Description

This function runs DeconRNAseq with default parameters such that it is compatible with CRAN and scMappR

Usage

DeconRNAseq_CRAN(
  datasets,
  signatures,
  proportions = NULL,
  checksig = FALSE,
  known.prop = FALSE,
  use.scale = TRUE,
  fig = FALSE
)

Value

DeconRNAseq_CRAN Estimated cell-type proportions with DeconRNAseq.

Arguments

datasets

Normalized RNA-seq dataset

signatures

Signature matrix of odds ratios

proportions

If cell-type proportion is already inputted - always NULL for scMappR

checksig

Check to see if plotting is significant - always false for scMappR

known.prop

If proportions were known - always false for scMappR

use.scale

Scale and center value - always TRUE for scMappR

fig

Make figures - always FALSE for scMappR

Details

This is the exact same function as the primary function in the Bioconductor package, DeconRNAseq (PMID: 23428642) except it is now compatible with CRAN packages.

Examples

# \donttest{
data(PBMC_example)
bulk_DE_cors <- PBMC_example$bulk_DE_cors
bulk_normalized <- PBMC_example$bulk_normalized
odds_ratio_in <- PBMC_example$odds_ratio_in
out <- DeconRNAseq_CRAN(datasets = as.data.frame(bulk_normalized),
                       signatures = as.data.frame(odds_ratio_in))
# }