Package index

CACTI peak-window cQTL mapping pipeline

cacti_run_chr()

Run CACTI peak-window pipeline for a single chromosome

cacti_run_genome()

Run CACTI peak-window pipeline genome-wide and add FDR

CACTI-S (Segment-based data preparation & mapping)

cacti_s_prep()

Run CACTI-S Prep Pipeline

Building blocks

Low-level functions for segmentation, counting, preprocessing, grouping, and testing.

cacti_group_peak_window()

Group adjacent peaks by non-overlapping windows

cacti_pheno_cov_residual()

Residualize peak intensity with covariates

cacti_cal_p()

Run CACTI association test for a single chromosome

cacti_add_fdr()

Add FDR (q-values) to per-window top hits across chromosomes

cacti_s_create_segments()

Create fixed-size genomic segments (SAF format)

cacti_s_count()

Count reads in genomic segments (CACTI-S)

cacti_s_preprocess()

Preprocess CACTI-S Segments

cacti_s_map_cis()

Run Nominal Cis-QTL Mapping (CACTI-S)