39  Genetic Data in R and GDS

39.1 Genetic Data in R and GDS lecture

Here’s a recording of this lecture (50 minutes 56 seconds):

Recording

39.2 Genetic Data in R and GDS slides

PDF slide set

39.3 Questions

39.3.1 Question 1

Which of the following are true? Select the correct options (more than one may be correct).

seqArray GDS and SNP GDS files are completely interchangeable, and all functions that work with one format will work with the other they are not interchangeable, but they can be easily converted into each other with plink They are not interchangeable, but they can be easily converted into each other with the seqArray package. plink files can be converted into GDS files using the seqArray package

39.3.2 Question 2

How do you open, close, and save GDS files in R?

read.table and write.table fread and fwrite BEDMatrix seqGDS2VCF seqOpen, seqClose, and seqExport

39.3.3 Question 3

How do you access data in a GDS object after opening it?

the dollar-sign operator piping redirection square brackets seqGetData and other built-in accessor functions double square brackets

39.3.4 Question 4

How would you filter a GDS object and then save the filtered data to a new GDS file?

seqGetFilter and then seqExport seqSetFilter and then seqClose seqSetFilter and then seqExport seqSetFilter and then write.table

39.3.5 Question 5

Which of the following are true? Select all that apply.

GDS files cannot store the same information as a VCF file GDS files are more flexible than plink file formats GDS files are smaller and more efficient than plink and VCF files GDS files integrate with specialized packages for GWAS data cleaning, kinship and population structure calculations, and association analysis When GDS files are opened, the entire dataset is read into memory seqArray cannot be used to convert from VCF to GDS and from GDS to VCF plink can be used to convert from plink to VCF and from VCF to plink