junctionAlignment {alakazam} | R Documentation |
Calculate junction region alignment properties
Description
junctionAlignment
determines the number of deleted germline nucleotides in the
junction region and the number of V gene and J gene nucleotides in the CDR3.
Usage
junctionAlignment(
data,
germline_db,
v_call = "v_call",
d_call = "d_call",
j_call = "j_call",
v_germline_start = "v_germline_start",
v_germline_end = "v_germline_end",
d_germline_start = "d_germline_start",
d_germline_end = "d_germline_end",
j_germline_start = "j_germline_start",
j_germline_end = "j_germline_end",
np1_length = "np1_length",
np2_length = "np2_length",
junction = "junction",
junction_length = "junction_length",
sequence_alignment = "sequence_alignment"
)
Arguments
data |
|
germline_db |
reference germline database for the V, D and J genes.
in |
v_call |
V gene assignment column. |
d_call |
D gene assignment column. |
j_call |
J gene assignment column. |
v_germline_start |
column containing the start position of the alignment in the V reference germline. |
v_germline_end |
column containing the end position of the alignment in the V reference germline. |
d_germline_start |
column containing the start position of the alignment in the D reference germline. |
d_germline_end |
column containing the start position of the alignment in the D reference germline. |
j_germline_start |
column containing the start position of the alignment in the J reference germline. |
j_germline_end |
column containing the start position of the alignment in the J reference germline. |
np1_length |
combined length of the N and P regions between the V and D regions (heavy chain) or V and J regions (light chain). |
np2_length |
combined length of the N and P regions between the D and J regions (heavy chain). |
junction |
column containing the junction sequence. |
junction_length |
column containing the length of the junction region in nucleotides. |
sequence_alignment |
column containing the aligned sequence. |
Value
A modified input data.frame
with the following additional columns storing
junction alignment information:
-
e3v_length
: number of 3' V germline nucleotides deleted. -
e5d_length
: number of 5' D germline nucleotides deleted. -
e3d_length
: number of 3' D germline nucleotides deleted. -
e5j_length
: number of 5' J germline nucleotides deleted. -
v_cdr3_length
: number of sequence_alignment V nucleotides in the CDR3. -
j_cdr3_length
: number of sequence_alignment J nucleotides in the CDR3.
Examples
germline_db <- list(
"IGHV3-11*05"="CAGGTGCAGCTGGTGGAGTCTGGGGGA...GGCTTGGTCAAGCCTGGAGGGTCCCTGAGACT
CTCCTGTGCAGCCTCTGGATTCACCTTC............AGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAG
GGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGT......AGTAGTTACACAAACTACGCAGACTCTGTGAAG
...GGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGA
CACGGCCGTGTATTACTGTGCGAGAGA",
"IGHD3-10*01"="GTATTACTATGGTTCGGGGAGTTATTATAAC",
"IGHJ5*02"="ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"
)
db <- junctionAlignment(SingleDb, germline_db)