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Variant Discovery & KASP Marker Design
query_db()
Query any table in your SQLite database using chromosome and a genomic position range.
query_by_af()
Extract variants based on minimum and maximum allele frequencies within a defined region in a SQLite database.
query_ann_summary()
Query the annotations table within a specified genomic region and summarize the distribution of SnpEff annotations and impact categories by variant type.
kasp_marker_design()
Design KASP markers based on causal variants.
list_sqlite_tables()
List all tables in the SQLite database.
variant_stats()
Get variants statistics stored in SQLite database
variant_impact_summary()
Get variants statistics stored in SQLite database based on mutation impact.
summarize_sqlite_tables()
Name and row count for each table in SQLite database.
list_table_columns()
Check the column names and types for any table in a SQLite database.
gene_coord_gff()
Get the genomic range of a candidate gene using the Sobic ID from a gff file.
query_by_impact()
Extract variants from annotation table based on impact type: LOW, MODERATE, HIGH, MODIFIER.
calc_af()
Compute allele frequencies for a VCF genotype matrix (variant x samples). Chromosome and position may be included in the data.
filter_by_af()
Filter extracted variants based on alternate allele frequency.
query_genotypes()
Query genotypes for one or more variant IDs from a wide-format genotype table.
count_variant_types()
Count the number of variant types in the SQLite database.
extract_variant()
Extract putative causal variants within a candidate gene from a tabix-indexed snpEff annotated VCF file.
get_google_id()
Get the folder or file ID from a Google Drive shareable link.
folder_download_gd()
Download files in a shared Google Drive folder without restrictions.
read_kasp_csv()
Read raw KASP results file (csv format) with one or multiple plates.
get_alleles()
Get SNP or InDel alleles and possible genotypes from genotype calls in KASP data.
kasp_pch()
Generate pch characters for cluster plots of KASP genotype calls.
kasp_color()
Color-code KASP genotype calls based on LGC genomics colors for HEX and FAM.
scale_axis()
Normalize FAM and HEX fluorescence values between 0 and 1
pred_status()
Generate the prediction status of positive controls in a KASP assay, if present.
pred_summary()
Generate summary of prediction for positive controls in KASP genotype data, if present
kasp_qc_ggplot()
Make KASP marker genotyping QC plot.
kasp_qc_ggplot2()
Make KASP marker genotyping QC plot overlaid with predicitons.
plot_plate()
Plot kasp genotyping plate layout.
nsamples_plate()
Get a summary of the number of samples per 96-well plate in a multi-plate KASP assay.
kasp_reshape_wide()
Reshape KASP data to wide format for same samples genotyped with multiple KASP markers.
proc_kasp()
Process reshaped KASP genotype data for heatmap plotting
geno_error()
Identify SNP loci with potential genotype call errors.
kasp_numeric()
Convert processed KASP data to numeric genotypes
pred_summary_plot()
Create decision support bar plots of match vs. mismatch rates of KASP markers that had predictions for positive controls.
gg_dat()
Convert data matrix for genotypes to a long format data frame.
Decision Support for MABC and Trait Introgression
parse_marker_ns()
Parse marker names of Hapmap format with a common pattern containing chromosome numbers and positions into a map file.
cross_qc_ggplot()
Create a heatmap to visualize and compare the genetic genetic backgrounds of genotypes/lines.
rm_mono()
Remove or filter out monomorphic loci from a data matrix or frame.
calc_rpp_bc()
Calculate the proportion of recurrent parent background (RPP) fully recovered in backcross progenies.
calc_rpp_exp()
Compute theoretical RPP values for any specified backcross generation.
rpp_barplot()
Visualize computed RPP values for BC progenies as a bar plot.
cross_qc_annotate()
Annotate start and end positions of loci on a heatmap.
cross_qc_heatmap()
Create a heatmap to visualize and compare the genetic genetic backgrounds of genotypes/lines with or without annotation for introgressed loci.
cross_qc_heatmap2()
Visualize genotype backgrounds with optional QTL annotations.
sim_snp_dat()
Simulate raw SNP loci for any chromosome with or without LD.
order_markers()
Order marker IDs based on their chromosome numbers and positions in ascending order.
hapmap_ns_fmt()
Format marker names to comply with the Hapmap convention.
find_unexp_homs()
Find loci with unexpected homozygous genotype calls for artificial heterozygotes.
find_indels()
Identify and subset InDel markers from a marker panel.
parent_missing()
Identify and subset loci with any parent missing genotype.
parent_het()
Identify and subset loci with any heterozygous parent genotype.
parent_poly()
Select polymorphic loci between two parents in a marker panel.
foreground_select()
Identify lines that possess favorable alleles for target loci using trait predictive markers.
find_lines()
Extracts lines that have a combination of favorable alleles across target loci.
