Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • filtering variants with R

    Hi,

    I'm learning basic data analysis with R, I'm using RStudio. I have my sequencing data in one file. It contains samples from 3 tissues from 100 individuals. I need to filter out variants within individuals, so that I can see variants unique for each tissue and common between two or all tissues.
    My file is one dataset with 116 columns - after filtering variants I would like to keep all the columns. One of these columns is my individual ID (for 130 individuals) and there are separate columns with variants and tissue types.
    So far, I understand that I need to create a loop that will filter within each individual by 1. sorting variants 2. apply filtering to variant presence in different tissues, so that in the end I would get: 1. 3 sets of variants unique for each tissue type, 2. 1 set of variants common to all tissue types, 3. 3 sets of variants common between 2 tissue types.

    I've tried the VennDiagram package, but it sorts out variants that occur in any other individual in my dataset. I need to look into variants in a single individual.

    Does anyone here know how to solve this??

    Cheers,
    A.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X