SNP-gene matrix construction

What is the easiest way to build an SNP-gene matrix, with rows corresponding to SNPs and columns corresponding to genes regulated by the SNP? Any insight would be much appreciated.

snp gene r

• 752 views • link

written 7.6 years ago by bioinfo456 15

R ? https://cran.r-project.org/web/packages/seqminer/index.html

Python ?

C: parsing vcf file

• 1 views • link

written 7.6 years ago by Bastien Hervé 680

0 answers

No answers yet.

More posts like this

RangedSummarizedExperiment to Sparse Matrix
written 3.5 years ago by rbronste 42

Looking to make a sparse matrix from a RangedSummarizedExperiment object with with regions as rows and cells as columns. The corresponding cell and region names …
How to plot two heatmaps with the same cell height and width for two different Matrix (same column …
written 4.6 years ago by FantasticAI 6

Hi I have two different matrix with the same column number but different row number. I would like to know if there is a general …
Searching for genes in assembles genome database
written 6.7 years ago by anabaena 1

Hey all, I am currently working on a project that requires searching for homologous genes in a large assembled meta-genome database. Instead of looking for …
Venn diagram with rows of multiple choices
written 6.9 years ago by avino 2

Hi there, I have two list of genes in two columns of a database, my goal is finding what is in common between the two …
Looking for human reference genome with ancestral SNP alleles
written 7.8 years ago by Scott 11

Hi. I am looking for reference human genome fasta files (preferably hg38) where the SNP alleles contributing to the reference sequence are always the ancestral …
Alzheimer's disease and its classification
written 7.9 years ago by bioinfo456 15

I'm interning on an Alzheimer's disease project where I'm asked to build a classification model to classify the same. As of now, I have a …
Question about selection of pathways to inhibit
written 7.9 years ago by rob.costa1234 32

I have an RNAseq results of drug treated vs control cells and performed pathways analysis with Up an down regulated genes. What I am trying …
differential expression analysis
written 8.5 years ago by bioinfo456 15

I have the data contained in an excel format (ie; gene ids, samples, corresponding gene counts). Can somebody please explain to me how i can …
Remove columns and rows which have only NAs without deleting all the data
written 9.2 years ago by ElenaL 0

Hi everyone, I am not entirely new in R but somehow the following problem bugs me for days now. I have a pairwise correlation matrix …
How to compute a correlation matrix from ternary variables?
written 11.0 years ago by Pas 3

Hi all, I have a matrix of genes whose expression is coded in a ternary system: -1 (down regulated), 0 (no detection) and 1 (up-regulated). …