Man pages for markgene/sjmat
St Jude Methylation Array Toolkit (SJMAT)

cnvRun CNV
cnv_pipelineCNV pipeline
collate_idat_tableCollate IDAT table
combine_targetsCombine query targets with reference targets
create_cnv_annoCreate annotations for CNV analysis
create_conumee_annoCreate Conume annotation of 'CNV.anno' class
create_idat_tableCreate IDAT table
create_query_listCreate query sample list
create_referenceCreate reference
create_report_dirCreate report directory
download_example_idat_filesDownload example IDAT files from GEO
get_detail_regionsGet detail regions
get_idat_fileGet IDAT files of a GEO sample (GSM) from GEO
get_idat_tableGet IDAT table
get_sample_sheetGet sample sheet
IdatTable-classAn S4 class to represent IDAT table
import_rnbImport RnBeads
join_sample_sheet_idat_tblJoin sample sheet to IDAT table
load_objectLoad an object from Rda file
MAAP-classAn S4 class to represent Methylation Array Analysis Pipeline
maap_exampleMAAP object example
pipePipe
pipelinePipeline
pipeline_examplePipeline example
plot_detailPlot detail view of Conumee analysis result
plot_genomePlot genome view of Conumee analysis result
qc_pipelineQC pipeline
read_experimentReads an entire metharray experiment using a sample sheet
read_sample_sheetRead a sample sheet
report_conumee_resultReport Conumee analysis result
rnb_pipelineRnBeads pipeline
run_conumeeConnumee wrapper of fit, bin, detail and segment steps
write_cnv_resultWrite sample CNV result
write_conumee_resultOutput Conumee analysis result as table
write_qc_resultWrite QC result
write_resultWrite result
markgene/sjmat documentation built on April 26, 2018, 4:13 p.m.