summariseAAPosition.RdList HLA alleles and amino acid residues at a given position.
summariseAAPosition(hla_calls, aa_pos, aln = NULL, na.rm = FALSE)HLA calls data frame, as returned by
readHlaCalls function.
String specifying gene and amino acid position, example
"A_9".
Matrix containing amino acid sequence alignments as returned by
readHlaAlignments function. By default function will use
alignment files shipped with the package.
Logical flag indicating if NA values should be considered
for frequency calculations.
Data frame containing HLA alleles, their corresponding amino acid residues and frequencies at requested position.
summariseAAPosition(MiDAS_tut_HLA, "A_9")
#> HLA-A (9)
#> 1 F
#> 2 S
#> 3 T
#> 4 Y
#> HLA-A alleles
#> 1 *01:01, *01:234, *01:237, *01:274, *01:98, *02:01, *02:02, *02:03, *02:07, *02:211, *02:22, *02:60, *02:614, *02:642, *02:686, *02:753, *02:763, *03:01, *03:02, *03:24, *03:312, *24:104, *31:21, *32:01, *32:02, *32:116, *74:01
#> 2 *01:02, *03:72, *11:88, *23:01, *23:17, *23:18, *24:02, *24:03, *24:04, *24:07, *24:20, *24:95, *26:16, *30:01, *30:02, *30:04
#> 3 *03:205, *11:43, *29:01, *29:02, *29:119, *31:01, *31:08, *33:01, *33:03, *33:05, *33:125, *33:163
#> 4 *01:43, *02:05, *02:06, *02:08, *02:10, *02:324, *11:01, *11:02, *11:03, *11:12, *11:306, *11:50, *24:50, *25:01, *25:09, *25:25, *26:01, *26:02, *26:03, *26:08, *33:51, *34:01, *34:02, *66:01, *68:01, *68:02, *68:04, *68:16, *68:164, *68:17, *68:23, *68:66, *69:01
#> count frequency
#> 1 1037 51.85%
#> 2 379 18.95%
#> 3 155 7.75%
#> 4 429 21.45%