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| check_raw | Check raw data |
| cnv | Copy Number Variation |
| filter_cnv | Filter Copy number variations |
| filt_samp | Filter Samples |
| filt_snps | Filter SNPs |
| filt_snps.norm_data | Filter SNPs |
| filt_snps.raw_data | Filter SNPs |
| find_blocks | Find Synteny Blocks |
| geno_baf_rratio | Genotype with kmeans using three clusters |
| intens_theta | Preprocess raw values and calculate Intensity and Theta values |
| plot_cnv | Plot Copy Number Variations |
| plot_global | Plot all chromosomes of a population |
| plot_gsr | Plot all chromosomes of a sample |
| plot_raw_snp | Plot raw SNP |
| plot_samp | Plot all chromosomes of a sample |
| plot_trans_locations | Plot translocations |
| read_intensities | Read multiple idat files. |
| read_sample_sheets | Read sample sheet(s) |
| remove_suffix | Remove suffix from sample names |
| rename_samples | Rename sample names |
| rename_samples.norm_data | Rename sample names |
| rename_samples.raw_data | Rename sample names |
| segm | Segmentation of R ratio values |
| synteny_info | Class for synteny information |
| trans_location | Find translocations |