Man pages for metamaden/recountmethylation.pipeline
Process DNAm array IDATs into database files
| append_md | Append metadata to DNAm data compilations |
| append_md_h5db | Append metadata to HDF5 DNAm data compilation file |
| append_md_h5se | Append metadata to HDF5-SummarizedExperiment DNAm data... |
| append_md_snakemake | Append metadata to compilation files |
| appendvar | Append mapped terms to a metadata variable |
| check_h5_database | Check DNAm data contained in an HDF5 database |
| control_biotinstaining | Biotin staining metrics |
| control_bsconversion | Bisulfite conversion I and II |
| control_extension | Extension metrics |
| control_hybridization | Hybridization metrics |
| control_nonpolymorphic | Non-polymorphic metric |
| control_restoration | Restoration metric |
| control_specificity | Specificity metrics |
| control_targetremoval | Target removal metrics |
| data_mdpost | Retrieve samples metadata from HDF5 db. |
| df_bathresh | Get minimum thresholds for BeadArray controls |
| do_h5se_merge | Merge 2 h5se objects with all pdata columns |
| dtables_rg | Get red and grn signal data tables |
| dt_checkidat | Validate idats at path, returns gsmu and hlinkv |
| dt_makefiles | Make and manage data.table files for red and grn signal |
| dt_write_rg | Write red and grn signal data to flat tables. |
| get_all_md | Get available metadata as a single table |
| get_atables | Generate study annotation tables |
| get_background | Get the background address from control probe data |
| get_bactrl | Get control probe metrics from matrices of red/grn signal |
| get_bathresh | Get BeadArray control outcomes from a matrix of metric... |
| getblocks | Get list of index blocks |
| get_eqfpath | Get an edirect query file path |
| get_filt | Get the outcome of pattern matching a string with regex... |
| get_gsm_exclude | Get GSM IDs to exclude for this instance |
| get_h5db_gm | Get HDF5 database of methylated/unmethylated signals, from... |
| get_h5db_gr | Get HDF5 database of DNAm fractions, from h5se rg data |
| get_h5db_rg | Get HDF5 database of red/green signals, from compilation data... |
| get_h5se_gm | Get HDF5-SummarizedExperiment of methylated/unmethylated... |
| get_h5se_gr | Get HDF5-SummarizedExperiment of DNAm fractions, from h5se rg... |
| get_h5se_rg | Get HDF5-SummarizedExperiment of red/green signals, from h5... |
| get_idat_sizem | Get matrices of IDAT file sizes before and after performing 2... |
| get_jsontitle | Get sample titles |
| get_mddnam | Get DNAm-based metadata |
| get_mdmap | Get mapped metadata |
| get_metadata | Append metadata to HDF5 or SE object |
| get_msrap | Get the pipeline data files as a flat table |
| get_pstr | Get regex patterns for a string, or the affirmative match for... |
| get_pstr_neg | Get negative regex string mapping |
| get_qcmetrics | Get quality metrics from DNAm assays |
| get_replicates | Get likely sample replicates |
| get_rg_dtables | Get compiled data tables of red and green signals |
| h5_addmd | Append sample metadata to HDF5 or SE object |
| h5_add_tables | Add red or green signal data tables to an HDF5 database. |
| make_h5db_rg | Make and populate a new HDF5 database with red and green... |
| make_h5_gm | Make an HDF5 db file with MethylSet data, from an... |
| make_h5_gr | Make an HDF5 h5 file with GenomicRatioSet data, from an... |
| make_h5se_gm | Make an H5SE MethySet object from a MethySet HDF5 database... |
| make_h5se_gr | Make an h5se object from an h5se gr file |
| make_h5se_rg | make_h5se_rg |
| match1to2 | Match and combine 2 datasets |
| md_age_infol | Age terms to seed regex queries |
| md_age_unitl | Age unit terms to seed regex queries |
| md_agg | Aggregate available metadata tables |
| md_post_cancer | Cancer terms for tissue variable |
| md_post_cancertype | Cancer terms list for tissue variable |
| md_post_disease | Disease terms for disease variable |
| md_post_handle_age | Handle age term mappings for metadata postprocessing |
| md_post_leukemia | Leukemia terms list for disease variable |
| md_postprocess | Postprocess metadata prepared using md_preprocess() |
| md_post_storage | Storage condition terms for storageinfo variable |
| md_post_tissue | Non-blood terms list for tissue variable |
| md_post_tissue_blood | Blood terms list for tissue variable |
| md_predictions | Make model-based metadata predictions |
| md_preprocess | Preprocess sample metadata |
| mdpre_vars | Get the regex patterns for variable mappings |
| mdpre_vars_age | Terms vector for variable age |
| mdpre_vars_disease | Terms vector for variable disease |
| mdpre_vars_info | Terms vector for variable info |
| mdpre_vars_sex | Terms vector for variable sex |
| mdpre_vars_tissue | Terms vector for variable tissue |
| new_instance_md | Get new instance metadata |
| rmp_handle_metadata | Get instance metadata info |
| rmp_handle_platform | Get instance platform info |
| se_addpheno | Append phenotype data to a SummarizedExperiment object |
