classify.nmd: Classify NMD-elicit mutations
In zhiyuanhu/masonmd: Make Sense of Nonsense-Mediated Decay

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; `ref = 37` if the mutation is called by build37/hg19, or `ref = 36` if the mutation is called by build36/hg18
`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; `ref_nt = "-"` for insertion
`mut_nt`	charactor; the mutation nucleotides on + strand; `mut_nt = "-"` for deletion

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

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")