Package index • mixder

All functions

check_allele_probabilities(): Checks EFM predicted genotypes for errors

add_rows(): Add SNPs to ensure same SNPs are present in both samples for a replicate analysis.

ancestry_1000G_allsamples: 1000 Genomes genotypes for 10,030 autosomal SNPs for all 2,504 1000G samples

ancestry_colors: Colors for creating 3D PCA plots

ancestry_prediction(): Ancestry prediction using PCA

ancestrysnps_1000G_allsamples: 1000 Genomes genotypes for 54 ancestry SNPs for all 2,504 1000G samples

assigned_A2(): Calls allele 2 based on established threshold

calc_metrics(): Calculating metrics for a single set of allele 1 and allele 2 probability thresholds

calculate_at(): Calculate the analytical threshold

centroids(): Centroid Calculations and Plotting

check_3_or_4_col(): Adds additional columns if necessary to data frame to ensure same number of columns between sample and replicate

check_allele_calls(): Checks EFM predicted genotypes for errors

check_nas(): Checks if entire column has NA values

check_ratios(): Check the mixture ratios for potentially single source samples (or samples with very high mixture ratios)

check_reads(): Check SNP sets if all SNPs have 0 reads

checking_af(): Checking AF file for correct format; formatting if necessary

compile_metrics(): Compiling metrics for the range of allele 1 and allele 2 probablity thresholds

create_at(): Create AT table containing only SNPs contained in the evidence file

create_config(): Create configuration file containing all settings for a specific run

create_evid(): Create evidence files for EFM mixture deconvolution

create_evid_all(): Creating SNP sets from evidence samples containing all SNPs

create_gedmatchpro_report(): Create GEDmatch PRO report

create_replicatedf(): Creates replicate df

decode_freq_name(): Convert frequency file name

equalize_samples(): Equalize samples when using replicates

filter_alleles(): Filters the called genotypes based on the allele 1 and allele 2 probability thresholds

fix_columns(): Identifies if one sample has more columns than another; adds columns as needed.

format_af(): Formatting allele frequency files for use in EFM

format_ref(): Formatting reference file

gedmatch_metrics(): Calculate various metrics on the inferred genotype dataset to assist user in evaluating the final dataset

get_ids(): Get Reference IDs from either CSV file or Sample Reports

kintelligence_snp_positions: Kintelligence SNP positions file

load_freq(): Load in frequency data

load_kin_older(): Formatting Kintelligence Sample Reports created with UAS version <2.5

load_kin_uas25(): Formatting Kintelligence Sample Reports created with UAS version 2.5

mixder(): Run MixDeR

popFreq_1000G: Allele Frequency file using 1000G Phase 3 dataset

popFreq_AFR: Allele Frequency file using 1000G Phase 3 dataset for all AFR individuals

popFreq_AMR: Allele Frequency file using 1000G Phase 3 dataset for all AMR individuals

popFreq_EAS: Allele Frequency file using 1000G Phase 3 dataset for all EAS individuals

popFreq_EUR: Allele Frequency file using 1000G Phase 3 dataset for all EUR individuals

popFreq_SAS: Allele Frequency file using 1000G Phase 3 dataset for all SAS individuals

popFreq_gnomad: Allele Frequency file using gnomADv4 dataset

process_efm_files(): Process files created by EFM

process_kinreport(): Function to determine how to create the AT file

processing_evid_sample_reports(): Creating usable data frame from a Kintelligence Sample Report

processing_ref_sample_reports(): Processing Reference Sample Reports

read_in_table(): Read in dataset to run through EFM

reverse_comp(): Identifying SNPs that need to be reverse complemented

run_efm(): Running mixture deconvolution in EuroForMix

run_indiv_efm_set(): Running individual EFM SNP sets in parallel

run_mixder_ancestry(): run MixDeR using the CLI; ancestry prediction

run_mixder_metrics(): run MixDeR using the CLI; calculate validation metrics

run_mixder_report(): run MixDeR using the CLI; create GEDmatch PRO report(s)

run_workflow(): Run MixDeR workflow

snpinfo: SNP information json file

write_tables(): Write metrics tables