Using the R libraries to look at Phenotype data

These R-libraries are not recommended to be used anymore, as we have switched to using BigQuery. We are recommending you to use Code Snippets of R or Python for looking at the phenotype data. R-libraries below are not supported for DF10.

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Instructions on this can be followed more conveniently inside the SandBox.

You can load theses libraries direct from /finngen/shared to RStudio.

Step 1:

First you need to install the R package to map the code text translations, this says DF6 but can be used for later data freezes as it has not been changed:

NOTE - you will need to install the package for mapping the code translations - /finngen/shared/r_packages_df6v2/20201124_083730/files/R_packages_18112020/FGCodesMappings_1.0.0.tar.gz

Step 2:

Then the DF9 libraries can be found from here: (older DF locations listed below if needed).

/finngen/shared/fglongitudinaldatadf9/20220209_091456/files

Step 3:

Here the file README.md explains the contains of the folder, how to install the R-packages, and tutorials in Rmd format on how to start using them.

Tutorials include how to load the longitudinal, filter events of interest, append names to the medical codes, review goodness of the codes matching and produced basic reports. You can use the same tutorial to work with R6, R7 and R8 data.

Location of r-packages for Data Release R6

/finngen/shared/r_packages_df6v2/20201124_083730/files/R_pakages_18112020/FGLongitudinalDataDF6_1.0.0.tar.gz

Location of r-packages for Data Release R7

    /finngen/shared/df7rpackage/20210501_065704/files/FGLongitudinalDataDF7/FGLongitudinalDataDF7_1.0.0.tar.gz

Location of r-packages for Data Release R8

/finngen/shared/fglongitudinaldatadf8/20211008_070835/files/FGLongitudinalDataDF8_0.0.0.9000.tar.gz

Location of r-packages for Data Release R9

/finngen/shared/fglongitudinaldatadf9/20220209_091456/files/FGLongitudinalDataDF9_1.0.0.tar.gz