Description Usage Arguments Details Value Examples
classify.nmd
can detect the premature stop codon (PTC) and predict NMD-elicit mutations
based on three rules.
1 2 | classify.nmd(gene_id, ref = 37, mut_start, mut_end, ref_nt = "-",
mut_nt = "-")
|
gene_id |
numeric; gene Entrez ID |
ref |
numeric; reference genome/NCBI build; |
mut_start |
numeric; the absolution start position of the mutations on chromosome on + strand |
mut_end |
numeric; the absolution end position of the mutations on chromosome on + strand |
ref_nt |
charactor; the reference nucleotides of the mutations on + strand;
|
mut_nt |
charactor; the mutation nucleotides on + strand; |
classify the mutations into NMD or non-NMD, and return the position of premature stop codon in CDS
A list containing eight entries:
mut_nmd
whether the mutation is NMD-elicit.
note
extra explanation of the classification results.
wt_nmd
whether the wildtype CDS harbours PTC that is NMD-elicit.
PTC.Stop
the position of PTC.
have.ptc
if the mutated sequence harbours a PTC.
mutseq_length
length of the mutated coding sequences
last_exon_exon_junction
relative position of last exon-exon junction
n.exon
number of exons in the gene
1 2 3 4 5 6 7 | library(masonmd)
# an example of NMD-escape mutation from TCGA
classify.nmd(gene_id = 13, ref = 37, mut_start = 151545640, mut_end = 151545640,
ref_nt = "G",mut_nt = "T")
# an example of NMD-elicit mutation from TCGA
classify.nmd(gene_id = 2, ref = 37, mut_start = 9221429, mut_end = 9221429,
ref_nt = "G", mut_nt = "A")
|
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