score_rafei: Rafei inhibitory KIR scores
In bosefalk/CTUtools: Common R functions for DKMS CTU

Description Usage Arguments Value Source Examples

Calculates the Rafei scores for inhibitory / activating KIRs, adjusted version of Krieger scores - see publication below

1	score_rafei(df, count_2DS4N_as_2DS4 = FALSE, return_numeric = FALSE)

df

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")

count_2DS4N_as_2DS4

Default FALSE, if set to TRUE 2DS4 is considered present if 2DS4 or 2DS4N is present

return_numeric

Default FALSE, if set to TRUE returns the raw inhibitory and activating KIR scores also

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

rafei_inh_kl_matches_2cat
rafei_act_kl_matches_2cat
rafei_inact_kl_matches_2cat

If return_numeric is TRUE, also returns, as numeric:

rafei_inh_ikir_numeric
rafei_act_akir_numeric

Rafei et al, Role of killer cell immunoglobulin-like receptor (KIR)-ligand interactions to prevent relapse in patients (pts) receiving matched unrelated stem cell transplant (SCT) for acute myeloid leukemia (AML). Journal of Clinical Oncology 37, https://ascopubs.org/doi/abs/10.1200/JCO.2019.37.15_suppl.7049

# 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_rafei(dat)
score_rafei(dat, return_numeric = TRUE)