vignette example - multiOmics example - dataset

gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection

https://gabrielodom.github.io/pathwayPCA/

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vignette example - multiOmics example - dataset #60

Closed lxw391 closed 5 years ago

lxw391 commented 5 years ago

If we're to also illustrate copy number analysis, we'll need to save CNV data in the package, right?

since reading in CNV data took a long time, consider saving it as an RDS data in /data?

lxw391 commented 5 years ago

We will also need to save phenotype file and rnaseq data for KIRP example in the pacakge,

the merged dataset "KIRP_HiSeq_inner.csv" at ~\Ban and Odom - Bioconductor Package\Example Data\Xena Interaction Kidney\data
or should we read in the estimated PCs directly?

gabrielodom commented 5 years ago

@lxw391, please comment here with the detailed file names or object names you would like included in the vignette data. From inspecting you vignette, it appears that you need

ovCNV_aespcOut (page 8)
KIRP_HiSeq_inner.csv (page11)

Will these work? Any others?

lxw391 commented 5 years ago

for interaction example let's save kidney data (kidney_df) in .RDS format, it's much faster to read that in let's also save aespcOut.RDS to save computing time
for multi-omics example save CNV data (copyNumberClean_df) in .RDS format, it only took 0.4 sec to read in the .RDS file on my computer also save ovCNV_aespcOut.RDS

gabrielodom commented 5 years ago

Based on the vignette edits, I've added the ovarian copy number data (OV_surv_x_CNV2.RDS) and kidney RNAseq data (KIRP_Surv_RNAseq_inner.RDS) to inst/extdata/.