Man pages for markgene/yamat
Yet Another Methylation Array Toolkit
| control_probe_intensities | Get control probes and their raw intensities. |
| copy_number | Get copy number. |
| create_idat_table | Create IDAT table |
| dye_bias_correction | Dye-bias correction |
| get_bisulfite_converstion_type_1_green_qc | Get QC metric of bisulfite Conversion of type I probe design... |
| get_bisulfite_converstion_type_1_red_qc | Get QC metric of bisulfite Conversion of type I probe design... |
| get_bisulfite_converstion_type_2_qc | Get QC metric of bisulfite Conversion of type II probe design... |
| get_control_probe_qc_metrics | Get QC metrics of control probes. |
| get_detection_p_value_qc_metrics | Summarize detection p-values by sample. |
| get_extension_green_qc | Get QC metric of extension green probes. |
| get_extension_red_qc | Get QC metric of extension red probes. |
| get_gender | Get gender information to 'RGChannelSet'. |
| get_gse | Create 'RGChannelSet' object from GSE accession. |
| get_hybridization_green_qc | Get QC metric of hybridization probe. |
| get_idat_file_list | Get IDAT file list |
| get_nonpolymorphic_green_qc | Get QC metric of non-polymorphic green probes. |
| get_nonpolymorphic_red_qc | Get QC metric of non-polymorphic red probes. |
| get_qc_metrics | Get QC metrics. |
| get_restoration_qc | Get QC metric of restoration probe. |
| get_sentrix_id | Get Sentrix IDs. |
| get_sentrix_position | Get Sentrix position. |
| get_specificity_type_1_green_qc | Get QC metric of specificity of type I probe design green... |
| get_specificity_type_1_red_qc | Get QC metric of specificity of type I probe design red... |
| get_specificity_type_2_qc | Get QC metric of specificity of type II probe design probes. |
| get_staining_green_qc | Get QC metric of staining green probes. |
| get_staining_red_qc | Get QC metric of staining red probes. |
| get_target_removal_qc | Get QC metric of target removal probes. |
| ggsci_pal_d | ggsci pal discrete. |
| init_report | Initiate report directory. |
| is_annotated | Is an object of minfi classes annotated? |
| normalize | Normalization wrapper. |
| normalize.dkfz | Normalization DKFZ. |
| normalize.methylcnv | Normalization MethylCNV. |
| normalize.yamat | Normalization method yamat. |
| plot_beta_value_histogram_fill_by_sample | Beta value distribution histgram fill by sample. |
| plot_control_probes | Quality control plot of control probes in terms of raw... |
| qc | Quality control |
| qc_control_probes | Quality control |
| qc_pipe | QC pipeline. |
| read_metharray_exp | Read methylation array with EPIC v2 support. |
| remove_batch_effect | Remove batch effect. |
| remove_batch_effect_beta | Remove batch effect: beta value. |
| remove_batch_effect_cn | Remove batch effect: copy number |
| remove_batch_effect_mum | Remove batch effect: methylation and unmethylation signals. |
| set_annotation_epic_v2 | Set annotation for an object of minfi classes of EPIC v2... |
| write_qc_metrics_excel | Write QC metrics into Excel file. |
