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Questions tagged [genetics]

The scientific study of the principles of heredity and the variation of inherited traits among related organisms.

Genetics is the study of genes — what they are, what they do, and how they work. Genes inside the nucleus of a cell are strung together in such a way that the sequence carries information: that information determines how living organisms inherit various features (phenotypic traits). For example, offspring produced by sexual reproduction usually look similar to each of their parents because they have inherited some of each of their parents' genes. Genetics identifies which features are inherited, and explains how these features pass from generation to generation. In addition to inheritance, genetics studies how genes are turned on and off to control what substances are made in a cell-gene expression.

Nowadays, the genetics is interesting in computer science too. It can propose own advances and results of the investigations to describe the information interpretation for very complex objects and needed methods on the algorithmic level. For example, one gene can save value about one feature of the object, furthermore, using different methods of information coding we can expand properties of one gene whereby different shades. Also, considering gene on the abstract level of our understanding, we can build a very powerful system of equations which will be describing the object completely from different aspects.

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How to manipulate two pieces of a column?

I am working with some genetic data and one of my columns isn't in the format I want it to be. I don't know how much biology is talked about on here, but I am trying to fix how my amino acids are shown in my data. Amino acids obviously have a name…
neuron
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transform flat linear tree representation into memory tree representation

I have a string like this: *b+a-aQa and would like to transform it into an hierarchical tree structure like this: The tree would consist of nodes like this: public class TreeNode : ITreeNode { public string Expression { get; set; } public…
cs0815
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Replace a value and adding rows with if/for loop

I want replace Sire with new Id if Dam is NOT 0. And after that add a new row each time with new Id and Sex. For example, I need to replace 0 in first row as s1073 and add a new row in data as 1 s1073 0 0 2. Similarly if Dam is 0 and Sir is NOT 0…
user2808642
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Neo4j cypher query for X-chromosome ancestors

In genetic genealogy X-chromosome data is useful linking to certain ancestors. This is well illustrated at: X-DNA Inheritance Chart My Neo4j database has nodes for each Person and relationships connecting them of father and mother. Each node has a…
David A Stumpf
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How to make a break in the y-axis in a Manhattan plot, so that variants with a p value within a certain range are omitted form the plot?

I am using a modified qqman function to create a Manhattan plot and one of the peaks in my plot is extremely tall, making it almost impossible to see any of the close-to-threshold loci in detail. I would like to make a break in the Y-axis, so that…
ingridc
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How to load GEO methylation (450k) datasets without sample sheet provided?

I downloaded some Illumina 450k methylation datasets from Gene Expression Omnibus (GEO) The R Bioconductor packages minfi and ChAMP seem to require something called a "sample sheet" Most TAR files on GEO do not seem to contain such a sample sheet -…
Nicholas Syn
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creating map file in r

I would like to prepare my dataset for analysis in the Plink program, but I have no idea on how to create the MAP and PED file. I understand that I can create a PED file in R, but how do I create a MAP file in R? Can someone help me with…
Terence Ng
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Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1127 characters (max is 1000)

I'm running blastx on my de novo transcriptome assembly. While the program is still running I've been obtaining errors like this one: Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1127 characters (max is 1000) ...and…
Mafalda
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Extract the character around a symbol in R

I would like to extract the character around a symbol using R and sub. I have tried many regular expression but I'm not getting what I want. My vector: c("G>GA", "T>A", "G>A", "G>A", "A>T", "CT>C", "T>C", "T>C", "A>T", "T>C", "T>A", "A>G",…
user3186183
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Finding overlapping regions of chromosome with GRanges

I have a list of ranges of genomic regions derived from a series of patients. > head(dotoo) GRanges with 6 ranges and 3 metadata columns: seqnames ranges strand | Id CN Histology …
Isidor Lipsch
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Loop for taking sum of rows based on proximity to other non-NA rows

I have a dataset with 2 important columns, Position and Count. There are a total of 34,532 rows, but only 457 non-NA values in the Count column (every cell in Position column has a value). I need to write a loop to march down the rows, and if there…
user2895292
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How can I query a genetics database of SNPs (preferably with R)?

Starting with a a few human single nucleotide polymorphisms (SNPs) how can I query a database of all known SNPS such that I can generate a list (data.table or csv file) of the 1000 or so closest SNPS, weather or not the SNP is a tagSNP, and what the…
Farrel
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how to plot multiple histograms on the same graph from multiple DNA distance files?

I have 100 fasta files and I would like to plot overlapping histograms of genetic distance matrix to see how much overlap there is between bootstrap replicates of DNA data? I have figured out how to get ape to read each file using: files <-…
arvandam
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Conditional Insert of Rows

I have a unique dataset, a portion of which can be reproduced using: data <-…
mfk534
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Retrieving GWAS information with R

I am trying to get specific disease-related information from the GWAS catalog. This can be done directly from the website via a spreadsheet download. But I was wondering if I could possibly do it programmatically in R. Any suggestions will be…
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