CTUtools-package: CTUtools: Common R functions for DKMS CTU

In bosefalk/CTUtools: Common R functions for DKMS CTU

Description

Common R functions and reference data used by DKMS CTU.

Main functions

shorten_allele: Reduce a long allele string (i.e. "01:02:01:03g") down to fewer fields ("01:02")

KIR_first_field: Reduce a long KIR string down to only use the first field (i.e. "001+002|003")

KIR_present: Determine if a KIR is present or absent given a KIR string

HLA_C_classification: Classify two HLA-C alleles into a C1/C2 group

HLA_B_classification: Classify two HLA-B alleles into an overall group Bw6, Bw4-80I or -80T

KIR_det_GCN: Convert a KIR string (such as "004+003|006+010") into a Gene Copy Number

KIR_haplotype_Cen & KIR_haplotype_Tel: Centomeric and Telomeric KIR haplotypes (A/A, A/B etc)

KIR3DL1_HLA_B_inhibiting: Classifies KIR3DL1 and HLA-B into strong/weak/no inhibiting

KIR3DL1_3DS1_assignment: Classifies KIR 3DL1 & 3DS1 alleles into KIR3DL1-H, -L, -N

HLA_Supertype: Assigns a HLA allele to its Supertype (A01, A02 A24 etc)

Score functions

score_boelen_inhib: Boelen inhibitory score calculation

score_krieger: Krieger inhibitory and activating KIR score calculation

score_rafei: Rafei varation of Kreiger scores

Datasets

HLA_C_class_data: Reference data for C1 / C2 classification

HLA_B_class_data: Reference data for Bw6, Bw4-80I and Bw4-80T classification

NMDP: Reference data for expanding NMDP codes

ASSIGN_KIR3DL1: KIR3DL1/HLA-B Subtypes, from Bodreau et al

Superclass_HLA: Superclass allele assignment for HLA-A and HLA-B

Location

https://github.com/bosefalk/CTUtools

devtools::install_github("bosefalk/CTUtools")

bosefalk/CTUtools documentation built on Feb. 4, 2022, 4:10 p.m.