score_krieger: Krieger inhibitory KIR scores

In bosefalk/CTUtools: Common R functions for DKMS CTU

Description

Calculates the Krieger scores for inhibitory / activating KIRs - see publication below

Usage

score_krieger(df, count_2DS4N_as_2DS4 = FALSE)

Arguments

count_2DS4N_as_2DS4	Default FALSE, if set to TRUE 2DS4 is considered present if 2DS4 or 2DS4N is present
data.frame	with the following columns: KIR allele strings, named "kir_2DL1" or "kir2dl1" HLA-A, B and C allele string, either as one column named "hla_a", or as two "A1" "A2" C- and B- ligand class column, named "B_class" & "C_class" (or "hla_c_class.pat")

Value

data.frame with the following columns, all as numeric:

• kirl_score

• imkir_score

• wkir_score

Source

Krieger et al, Killer Immunoglobulin-Like Receptor-Ligand Interactions Predict Clinical Outcomes following Unrelated Donor Transplantations, Biol Blood Marrow Transplant. 2019 Oct 30, https://www.ncbi.nlm.nih.gov/pubmed/31676338

Examples

# Create example dataframe
dat <- structure(list(kir_2DL1 = 1L, kir_2DL2 = 1L, kir_2DL3 = "NEG", 
kir_3DL1 = "NEG", kir_3DL2 = 1L, kir_2DS1 = 1L, kir_2DS2 = "NEG", 
kir_2DS4 = 1L, kir_2DS4N = "NEG", kir_2DS5 = 1L, kir_3DS1 = 1L, 
C_class = "C1/C1", B_class = "Bw6/Bw4-80T", A1 = "01:01", 
A2 = "01:01", B1 = "01:01", B2 = "01:01", C1 = "01:01", C2 = "01:01"), class = "data.frame", row.names = c(NA, 
                                                                                                          -1L))
score_krieger(dat)

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