The `playbase´ package contains the core back-end functionality for the OmicsPlayground. This package allows you to run, develop, and test any essential functions used in the OmicsPlayground directly in the R console without needing to worry about the R Shiny front-end code.
You can install the development version of playbase from GitHub with:
# install.packages("devtools")
devtools::install_github("bigomics/playbase")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.
library(playbase)
# Here we check that your input files do not have problems
playbase::PGX_CHECKS # These are the possible errors you can encounter
# 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
pgx <- playbase::pgx.createPGX(
samples = playbase::SAMPLES,
counts = playbase::COUNTS,
contrasts = playbase::CONTRASTS
)
# Step 2. Populate pgx object with results
pgx <- playbase::pgx.computePGX(
pgx = pgx
)
The core object in playbase is the pgx object. This object holds the
raw data and any analysis results returned from playbase modules /
boards. The pgx object is simply an R list. It contains minimally the
following list items:
- counts
- samples
- contrasts
A pgx object is created from these three list items via the following function:
my_pgx <- pgx.createPGX(counts, samples, contrasts)
Once a pgx object is created from these three items, the various playbase modules can operate on the pgx object to generate the analysis results relevant to that specific module.
As mentioned above, the core object in playbase is the pgx object.
This holds all of the analysis and results derived from the raw data, as
well as the raw data itself. There are various modules in playbase that
take a pgx object as input, perform some analysis on the raw data in the
pgx object, and then append these results to the pgx object. These
modules are more-or-less independent of one another and can therefore be
parallelized or run in any arbitrary order.
The core playbase modules operate on either genes or genesets.
The gene modules are as follows:
- ttest
- ttest.welch
- ttest.rank
- voom.limma
- trend.limma
- notrend.limma
- edger.qlf
- edger.lrt
- deseq2.wald
- deseq2.lrt
The geneset methods are as follows:
- fisher
- gsva
- ssgsea
- spearman
- camera
- fry
- fgsea
And extra modules are as follows:
- meta.go
- deconv
- infer
- drugs
- graph
- connectivity
- wordcloud