Functions
BLAASD()
BLAASD() extracts alignment sequence information for a given locus from the ANHIG/IMGTHLA GitHub repository to produce a data frame of individual amino acid data for each amino acid position for all alleles. The first 4 columns are locus, allele, trimmed allele, and allele_name, as shown below.
Most DQ-Beta proteins (e.g., DQB1*05:01) lack the eight amino-acids encoded by exon 5 due to an intron 4 splice-acceptor mutation. Some DQB1 alleles (e.g., DQB1*05:03 and *06:01) do not have this intron mutation, and include these eight amino acids. However, because DQB1*05:01 is the DQB1 reference allele, these amino acid positions are represented as insertion positions in the protein alignment generated by the IPD-IMGT/HLA Database. It is not clear how these exon 5-encoded amino acid positions are numbered in the IPD-IMGT/HLA Database; BLAASD() assigns amino-acid position numbers 227-234 to these eight amino-acid indel positions, and the C-terminal DQB1 amino-acid position in the DQB1 protein alignment generated by BLAASD() is position 237.
The output for HLA-DRB3/4/5 will contain DRB1 information for the first row since the reference sequence derived for DRB3/4/5 is from DRB1 in the DRB alignment.
Example output of BLAASD() for HLA-A, where the selected row outputs are 2 and 8 to illustrate different HLA-A alleles, and selected columns are the first 19 columns of the dataframe, where the first 4 columns consist of the locus, allele, trimmed_allele of 2 fields, and the full allele name. The rest of the columns consist of corresponding amino acids for each amino acid position for a given allele:
>BLAASD("A")[[1]][c(2,8),1:19]
locus allele trimmed_allele allele_name -24 -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10
2 A 01:01:01:02N A*01:01 A*01:01:01:02N M A V M A P R T L L L L L S G
8 A 01:01:01:08 A*01:01 A*01:01:01:08 M A V M A P R T L L L L L S GfindMotif()
findMotif() parses the provided amino-acid motif, which should be written as locus*##$~##$~##$, where ## identifies a peptide position, and $ identifies an amino acid residue. Motifs can include any number of amino acids positions. The following output is an example of the first three DRB1 alleles that have the DRB1*26F~28E~30Y motif.
>findMotif("DRB1*26F~28E~30Y")[1:3,1:65]
locus allele trimmed_allele allele_name -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -17
204 DRB1 03:02:01 DRB1*03:02 DRB1*03:02:01 M V C L R L P G G S C M A
205 DRB1 03:02:02 DRB1*03:02 DRB1*03:02:02 * * * * * * * * * * * * *
206 DRB1 03:02:03 DRB1*03:02 DRB1*03:02:03 * * * * * * * * * * * * *
-16 -15 -14 -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
204 V L T V T L M V L S S P L A L A G D T R P R F L E Y S T S E C H F
205 * * * * * * * * * * * * * * * * G D T R P R F L E Y S T S E C H F
206 * * * * * * * * * * * * * * * * * * * * * R F L E Y S T S E C H F
18 19 20 21 22 23 24 25 26 INDEL-1 27 28 29 30 31
204 F N G T E R V R F . L E R Y F
205 F N G T E R V R F . L E R Y F
206 F N G T E R V R F . L E R Y FIf a motif is not found, a warning message is output:
>findMotif("DRB1*26F~28E~30Z")
Warning message:
In findMotif("DRB1*26F~28E~30Z") :
DRB1*26F~28E~30Z: No alleles possess this motifIf a motif has formatting errors, a warning message is output:
>findMotif("DRB1**27F")
Warning message:
In findMotif("DRB1**27F") :
Your motif is formatted incorrectly. Please use the Locus*##$~##$~##$ format, where ## identifies a peptide position, and $ identifies an amino acid residue.If a motif contains an amino acid position not present in the 3.39.0 ANHIG/IMGTHLA alignments, a warning message is output:
> findMotif("DRB1*27999F")
Warning message:
In findMotif("DRB1*27999F") :
One or more of your amino acid positions is not present in the alignment. Please make sure amino acid positions of interest are present in the current release of ANHIG/IMGTHLA alignments.PALM()
PALM() generates a frequency heatmap for an HLA amino-acid motif, based on the allele frequency data in the Solberg dataset, using the gmt R package and the Generic Mapping Tools (GMT) map-making software. GMT software is required for this function and can be downloaded at https://www.soest.hawaii.edu/gmt/.
JPEG heatmap files named “‘motif’.jpg”, where ‘motif’ is the value of the motif parameter, are written to a directory identified by the direct parameter, with the working directory set as the default. The file names of maps generated on Microsoft Windows systems have a different delimiter between the locus name and the amino acid positions; instead of an asterisk (*), a dash (-) is used to accomodate for Windows naming conventions (e.g. DRB1-26F~28E~30Y).
The filename parameter defaults to the solberg_dataset list object. The color and filter_migrant parameters default to TRUE. When color = TRUE, PALM generates a color heatmap; when color = FALSE, a greyscale heatmap is generated. When filter_migrant = TRUE, populations from the OTH region and populations with complexity values suffixed with ‘mig’ are excluded from the heatmap plot. When filter_migrant = FALSE, these populations are included in the heatmap plot.
The Ghostscript software suite (>= version 9.26) is required to generate the heatmap file. Versions of Ghostscript < 9.26 introduce a layering error during heatmap generation. To determine if maps are being generated correctly, compare heatmaps of the DRB1*26F~28E~30Y motif (with filter_migrant = TRUE) against the examples in this vignette.
Note: While the map legend identifies the highest frequency value, values in this range may not be represented on the map due to frequency averaging over neighboring populations.
#color heatmap plot
>PALM("DRB1*26F~28E~30Y")
…
#greyscale heatmap plot
>PALM("DRB1*26F~28E~30Y", color=FALSE)
…
#if an amino acid motif is not found in the Solberg dataset, a warning is output
>PALM("DRB1*-25R~13S~16H~26Y~47Y~86V")
Warning message:
In PALM("DRB1*-25R~13S~16H~26Y~47Y~86V") :
DRB1*-25R~13S~16H~26Y~47Y~86V : No alleles possess this motif