Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Left-normalisation of variants using R

    I'm writing a mitochondrial haplotyping script in R, and one of the things I needed to do was left-normalisation of INDELs. Because of the way the variants were originally defined, I'm using the notation <ref><pos><alt> for variants (e.g. ACCCCCTCTA8280A to describe a 9bp deletion at location 8280). Here's my script:

    Code:
    ## left-normalise INDELs                                                                                                                 
    ## derived from pseudocode from http://genome.sph.umich.edu/wiki/Variant_Normalization                                                   
    leftNorm <- function(ref.seq, ref, pos = NULL, alt = NULL){
        if(any(grepl("[0-9]",ref))){
            leftNorm(ref.seq=ref.seq,
                     ref=sub("^(.*?)([0-9]+)(.*)$","\\1",ref),
                     pos=as.numeric(sub("^(.*?)([0-9]+)(.*)$","\\2",ref)),
                     alt=sub("^(.*?)([0-9]+)(.*)$","\\3",ref));
        } else {
            equalRights <- (substring(ref,nchar(ref)) == substring(alt,nchar(alt)));
            while(sum(equalRights) > 0){
                substring(ref,nchar(ref))[equalRights] <- "";
                substring(alt,nchar(alt))[equalRights] <- "";
                emptyAlleles <- ((nchar(ref) == 0) | (nchar(alt) == 0));
                pos[emptyAlleles] <- pos[emptyAlleles] - 1;
                ref[emptyAlleles] <- paste0(substring(as.character(ref.seq),pos[emptyAlleles],pos[emptyAlleles]),
                                            ref[emptyAlleles]);
                alt[emptyAlleles] <- paste0(substring(as.character(ref.seq),pos[emptyAlleles],pos[emptyAlleles]),
                                            alt[emptyAlleles]);
                equalRights <- (substring(ref,nchar(ref)) == substring(alt,nchar(alt)));
            }
            leftChangeable <- (substring(ref,1,1) == substring(alt,1,1)) & (nchar(ref) >= 2) & (nchar(alt) >= 2);
            while(sum(leftChangeable) > 0){
                substring(ref[leftChangeable],1,1) <- "";
                substring(alt[leftChangeable],1,1) <- "";
                pos[leftChangeable] <- pos[leftChangeable] + 1;
                leftChangeable <- (substring(ref,1,1) == substring(alt,1,1)) & (nchar(ref) >= 2) & (nchar(alt) >= 2);
            }
            paste0(ref,pos,alt);
        }
    }
    Here's a little test, using the example from here:

    Code:
    > all(leftNorm("GGGCACACACAGGG",c("CA8","CAC6C","GCACA3GCA","GGCA2GG","GCA3G")) == "GCA3G");
    [1] TRUE
    Note that the code uses vectorisable functions, so should work equally well on single values and vectors. A bit more tweaking is needed to get it to do the right thing on matrices.

Latest Articles

Collapse

  • seqadmin
    Choosing Between NGS and qPCR
    by seqadmin



    Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
    10-18-2024, 07:11 AM
  • seqadmin
    Non-Coding RNA Research and Technologies
    by seqadmin




    Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

    Nobel Prize for MicroRNA Discovery
    This week,...
    10-07-2024, 08:07 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 11-01-2024, 06:09 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-30-2024, 05:31 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-24-2024, 06:58 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-23-2024, 08:43 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Working...
X