adult_gene_expression_analysis: Gene expression spatial enrichment

In DJFernandes/ABIgeneRMINC: Read, Write, and Analyzing Allen Gene Expression Raw Data

Gene expression spatial enrichment

Description

Conducts a gene expression spatial enrichment analysis for arbitrary anatomy statistics. Statistics above the target threshold constitute the target region-of-interest (ROI). Statistics below a contrast threshold constitute the contrast region. Gene expression spatial enrichment is calculated for any number of genes in the ABI gene expression atlas. Enrichments is computed using a fold-change measure: expression in target ROI divided by expression in contrast region. If contrast threshold is not suppled, then the contrast regions is assumed to be the whole brain.

Usage

adult_gene_expression_analysis(
  anatomy_statistics,
  gene_expression_paths = NULL,
  target_threshold,
  contrast_threshold = NULL,
  symmetric_statistics = F,
  ABI_registration = list(anatomy_template = NULL, anatomy_mask = NULL,
    allen_ccf3v_template = NULL, allen_ccf3v_mask = NULL, anatomy_transform = NULL),
  gene_expression_analyis_options = list(interpolate_gene = F, reflect_gene = T,
    brain_mask = NULL),
  tmp_files_dir = NULL,
  parallel = NULL,
  conf_file = getOption("RMINC_BATCH_CONF")
)

Arguments

anatomy_statistics	MINC file or vector denoting statistics at each voxel
gene_expression_paths	Filenames or URLs pointing to gene expression data. If NULL, then genome-wide gene expression analysis is conducted and gene expression data is downloaded to temporary files.
target_threshold	statistics greater than this value constitute the ROI
contrast_threshold	statistics less than this value constitute the contract region. If NULL, then contrast region is assumed to be the whole brain.
symmetric_statistics	Should the absolute value of statistics at each voxel be considered instead of the signed value?
ABI_registration	arguments that can be supplied if you want to perform a registration prior to analysis. If you provide an XFM filepath as 'anatomy_transform', then the statistics will be transformed and resampled prior to gene expression analysis. If you provide 'anatomy_template' (filepath or MINC vector denoting the anatomy where statistics were conducted), 'anatomy_mask' (filepath or MINC vector denoting brain mask for anatomy), then the anatomy is registered to the ABI template and the resulting transformation applied to the statistics prior to gene expression computation. In this case, ABI template and mask are downloaded unless 'allen_ccf3v_template' and 'allen_ccf3v_mask' point to filepaths containing the respective information.
gene_expression_analyis_options	options for gene expression analysis. 'interpolate_gene' flags whether nearest-neighbour imputation should be done to fill in missing gene expression voxels. If FALSE, then these voxels are ignored. 'reflect_gene' flags whether gene expression signal should be reflected across the sagittal midplane to fill in missing gene expression voxels in the opposite hemisphere. 'brain_mask' is a MINC file, RAW file, or vector identifying which voxels are in the brain. If NULL, the mask will be downloaded from the ABI.
tmp_files_dir	location to store temporary files from the registration
parallel	how many processors to run on (default=single processor). Specified as a two element vector, with the first element corresponding to the type of parallelization, and the second to the number of processors to use. For local running set the first element to "local" or "snowfall" for back-compatibility, anything else will be run with batchtools. Leaving this argument NULL runs sequentially.
conf_file	A batchtools configuration file defaulting to getOption("RMINC_BATCH_CONF")

Value

gene expression enrichment expressed as fold-change

DJFernandes/ABIgeneRMINC documentation built on March 21, 2022, 12:05 p.m.