Man pages for svenstringer/genematrix
Create a Table with Gene Annotation and Output in Convenient Format

add_annotationsAdd annotations to core gene matrix
add_to_symbol_tableSymbol
annotate_magmaCreate gene annotation file for MAGMA (and install MAGMA if...
check_pathChecks if path exists
compute_genebased_pCompute gene-based pvalue based on daner summary stats file
compute_genebased_pvaluesCompute gene-based pvalue based on daner summary stats files...
create_core_matrixCore matrix is a merge between gencode, entrez and hgnc data.
create_dirCreate directory if it does not exist
create_symbol_tableCreate gene symbol translation table
download_sourceDownload source url if it does not exist in destination path
generate_genematrixSave annotated Gene Matrix
get_core_matrixLoad core gene matrix and create it first if it does not...
get_magma_osversionGet compiled magma platform version to download: windows...
get_symbol_tableLoad gene name translation table and create if it does not...
gm_settingssymbol','aliases','strand','merge_trial',...
install_magmaInstall stand-alone magma if not available yet
is_parCheck whether a genomic position is in a PAR regions Assumes...
lookup_symbolLookup gene symbol in gene-translation-table (gtt)
merge_annotation_by_genenameMerge processed annotation file to gene matrix
merge_commonmindDLPFCMerge omim phenotypes to gene matrix
merge_core_entrezMerge gencode and hgnc file
merge_exacpliMerge exac pli constraint data into gene matrix
merge_gencode_hgncMerge gencode and hgnc file
merge_genebased_pvaluesCompute gene-based pvalue based on daner summary stats files...
merge_gwascatalogMerge exac pli constraint data into gene matrix
merge_omimMerge omim phenotypes to gene matrix
merge_snpnrsMerge nr of SNPs per gene used in gene-based test
merge_url_linksMerge url links to common resources
process_commonmindDLPFCProcess omim morbidmap.txt file (source...
process_entrezfilePreprocess entrez file as downloaded from...
process_exacpliProcess exac pli constraint file
process_gencodefilePreprocess gencode file
process_gwascatalogProcess exac pli constraint file
process_hgncfilePreprocess hgnc file as downloaded from...
process_omimProcess omim morbidmap.txt file (source...
publish_genematrixSave customized gene matrix based on settings
uniform_genenamesStandardize gene names to upper case and remove punctuations...
svenstringer/genematrix documentation built on May 26, 2017, 11:03 p.m.