DESeq2 and R commands

Question

[Harry_Potter]

I am just getting started with R and I am looking for differentially expressed genes between men and women. The problem is, as I browseVignettes, I find I am just copying commands and arguments without really knowing what they mean. For example, which(phenoData(lgg_data)$idh1_mutation_found=="Yes" is given as an example. The string has so many things going on, and being new to programming I am having a hard time. Is there a DESeq resource that goes through these commands and arguments? I have an R book, but it doesn't go into "phenoData" and "mutation" and these biological areas.

[WouterDeCoster]

Try this workflow from bioconductor, it will get you started and provides explanation on commands.

Answer 1

[dvanic]

1. Make sure you are using RStudio. It will make your overall experience of using R significantly easier and more pleasant.

2. You can and should use the ?command syntax to read a description of what the commands + arguments mean. So for example ? phenoData, ?which

3. which(phenoData(lgg_data)$idh1_mutation_found=="Yes")

Try breaking things down, and trying stuff out to see what it's made of. Commands like head(), str(), table() and summary()

For example, try doing head(phenoData(lgg_data)) or str(phenoData(lgg_data)) or summary(phenoData(lgg_data)). What happens?

Then try head(phenoData(lgg_data)$idh1_mutation_found) and summary(phenoData(lgg_data)$idh1_mutation_found) and table(phenoData(lgg_data)$idh1_mutation_found)

Hint "idh1_mutation_found" is actually the name of a column in phenodata which contains a factor.

R is hard, and so is bioinformatics. There is no way around googling and trying stuff, sorry. Or do all of the edX Xseries on biological data analysis with R - but this will take you > month and not solve your direct problem.

Answer 2

[ammarsabir15]

There are number of resources where you can know about these commands.I have listed these A youtube video describing Deseq

This is another blog

Also you can get about working of these commands from the manual of DESEQ given at This link

And specifically if you want to learn R for bioinformatics then there are also bundle of resources to do that just google and write

R for Bioinformatics, R for NGS Data Analysis

And welcome to programming.

[WouterDeCoster]

Your links all describe DESeq, while that package is replaced by DESeq2 and therefore should no longer be used.