Files in metamaden/recountmethylation.pipeline

Process DNAm array IDATs into database files

R/bacontrol_format.R R/get_gsm_exclude.R R/md_dnam.R R/md_misc.R R/md_msrap.R R/md_postprocess.R R/md_preprocess.R R/rmpipeline.R R/snakemake_functions.R R/utilities.R README.md inst/scripts/run_rmpipeline.R inst/snakemake/append_md.R inst/snakemake/do_dnam_md.R inst/snakemake/do_mdmap.R inst/snakemake/do_msrap.R inst/snakemake/get_gsm_exclude.R inst/snakemake/get_h5db_gm.R inst/snakemake/get_h5db_gr.R inst/snakemake/get_h5db_rg.R inst/snakemake/get_h5se_gm.R inst/snakemake/get_h5se_gr.R inst/snakemake/get_h5se_rg.R inst/snakemake/get_rg_compilations.R inst/snakemake/make_md_final.R inst/snakemake/new_instance_md.R inst/snakemake/run_dnam_pipeline.R man/append_md.Rd man/append_md_h5db.Rd man/append_md_h5se.Rd man/append_md_snakemake.Rd man/appendvar.Rd man/check_h5_database.Rd man/control_biotinstaining.Rd man/control_bsconversion.Rd man/control_extension.Rd man/control_hybridization.Rd man/control_nonpolymorphic.Rd man/control_restoration.Rd man/control_specificity.Rd man/control_targetremoval.Rd man/data_mdpost.Rd man/df_bathresh.Rd man/do_h5se_merge.Rd man/dt_checkidat.Rd man/dt_makefiles.Rd man/dt_write_rg.Rd man/dtables_rg.Rd man/get_all_md.Rd man/get_atables.Rd man/get_background.Rd man/get_bactrl.Rd man/get_bathresh.Rd man/get_eqfpath.Rd man/get_filt.Rd man/get_gsm_exclude.Rd man/get_h5db_gm.Rd man/get_h5db_gr.Rd man/get_h5db_rg.Rd man/get_h5se_gm.Rd man/get_h5se_gr.Rd man/get_h5se_rg.Rd man/get_idat_sizem.Rd man/get_jsontitle.Rd man/get_mddnam.Rd man/get_mdmap.Rd man/get_metadata.Rd man/get_msrap.Rd man/get_pstr.Rd man/get_pstr_neg.Rd man/get_qcmetrics.Rd man/get_replicates.Rd man/get_rg_dtables.Rd man/getblocks.Rd man/h5_add_tables.Rd man/h5_addmd.Rd man/make_h5_gm.Rd man/make_h5_gr.Rd man/make_h5db_rg.Rd man/make_h5se_gm.Rd man/make_h5se_gr.Rd man/make_h5se_rg.Rd man/match1to2.Rd man/md_age_infol.Rd man/md_age_unitl.Rd man/md_agg.Rd man/md_post_cancer.Rd man/md_post_cancertype.Rd man/md_post_disease.Rd man/md_post_handle_age.Rd man/md_post_leukemia.Rd man/md_post_storage.Rd man/md_post_tissue.Rd man/md_post_tissue_blood.Rd man/md_postprocess.Rd man/md_predictions.Rd man/md_preprocess.Rd man/mdpre_vars.Rd man/mdpre_vars_age.Rd man/mdpre_vars_disease.Rd man/mdpre_vars_info.Rd man/mdpre_vars_sex.Rd man/mdpre_vars_tissue.Rd man/new_instance_md.Rd man/rmp_handle_metadata.Rd man/rmp_handle_platform.Rd man/se_addpheno.Rd