Package index • RWisecondorX

All functions

COMPRESSED_BINSIZE: Compressed bin size for synthetic cohort BAMs
bam_convert(): Count reads per bin from a BAM or CRAM file
bam_convert_bed(): Convert BAM/CRAM to a bgzipped BED bin-count file
bam_convert_npz(): Convert BAM/CRAM to WisecondorX NPZ format
bed_to_nipter_sample(): Read a NIPTeR-format BED file into a NIPTeRSample
bed_to_sample(): Read a WisecondorX-format BED file into a sample list
generate_cohort(): Generate a synthetic BAM cohort for testing
nipter_as_control_group(): Build a NIPTeR control group from a list of binned samples
nipter_bin_bam(): Bin a BAM/CRAM file — NIPTeR style
nipter_bin_bam_bed(): Write NIPTeR-style bin counts to a bgzipped BED file
nipter_chi_correct(): Chi-squared correction for overdispersed bins
nipter_control_group_from_beds(): Load a NIPTeR control group from a directory of TSV.bgz files
nipter_diagnose_control_group(): Diagnose a NIPTeR control group
nipter_gc_correct(): GC-correct a NIPTeR sample or control group
nipter_gc_precompute(): Pre-compute and save per-bin GC content to a TSV.bgz file
nipter_match_control_group(): Select best-matching controls for a sample
nipter_match_matrix(): Compute the full pairwise SSD matrix for a control group
nipter_ncv_score(): Normalised Chromosome Value (NCV) score
nipter_predict_sex(): Predict fetal sex for a NIPTeR sample
nipter_regression(): Regression-based Z-score for trisomy prediction
nipter_sex_model(): Build a sex prediction model from a NIPTeR control group
nipter_sex_model_y_unique(): Build a sex prediction model from Y-unique ratios
nipter_y_unique_ratio(): Compute Y-unique region read ratio from a BAM file
nipter_z_score(): Chromosomal Z-score
rwisecondorx_newref(): Build a WisecondorX reference from binned samples
rwisecondorx_predict(): Predict copy number aberrations using WisecondorX
scale_sample(): Scale a binned sample to a new bin size
sra_runinfo_url() download_sra_runinfo() read_sra_runinfo(): SRA Run Metadata Utilities
wisecondorx_convert(): Convert BAM/CRAM to WisecondorX NPZ format (upstream CLI wrapper)
wisecondorx_newref(): Build a WisecondorX reference panel
wisecondorx_predict(): Predict copy-number aberrations with WisecondorX
write_wisecondorx_output(): Write prediction output files