What if I have many datasets?¶

The first step in any OmicsPlayground analysis is to upload data which can be used to create a pgx object. The pgx object is basically the core data structure in the OmicsPlayground upon which most analysis and plotting functions operate.

If you have many datasets (tens to hundreds), it might make sense to create the pgx object with an R script.

We made it very easy to create a pgx object from your own data. With a few R functions, you can convert several datasets into pgx objects that can be uploaded in Omics Playground.

Here we check that your input files do not have problems

# install necessary packages

install.packages("devtools")
devtools::install_github("bigomics/playbase")

library(playbase)

# These are the possible errors you can encounter

playbase::PGX_CHECKS

# individual file checks

SAMPLES = playbase::pgx.checkINPUT(playbase::SAMPLES, type = "SAMPLES")
COUNTS = playbase::pgx.checkINPUT(playbase::COUNTS, type = "COUNTS")
CONTRASTS = playbase::pgx.checkINPUT(playbase::SAMPLES, type = "CONTRASTS")

# Checks across input files

INPUTS_CHECKED <- pgx.crosscheckINPUT(SAMPLES, COUNTS, CONTRASTS)

SAMPLES = INPUTS_CHECKED$SAMPLES
COUNTS = INPUTS_CHECKED$COUNTS
CONTRASTS = INPUTS_CHECKED$CONTRASTS

If no errors are reported (and PASS is TRUE), these new checked files SAMPLES, COUNTS and CONTRASTS can be used safely in the next step.

Here we create a pgx object that can be used in Omics Playground:

# step 1: create a pgx object with your samples, counts and contrasts
pgx <- playbase::pgx.createPGX(
  counts = playbase::COUNTS,
  samples = playbase::SAMPLES,
  contrasts = playbase::CONTRASTS
)

# step 2: compute the pgx object

pgx <- playbase::pgx.computePGX(
  pgx = pgx
)

# save the pgx object to your computer
save(pgx, file = "choose_a_name.pgx.")

All you have to do is substitute playbase::COUNTS, playbase::SAMPLES, and playbase::CONTRASTS with your own data. You can then import the pgx object into Omics Playground.