selectProjectsByCharacteristics: Select Recount projects based on the presence of...

In elqumsan/RNAseqMVA: Application of Multivariate Analysis methods to RNA-seq Data

Description

Recount metadata contains a field named "characteristics", which is a list of fields with values. It is useful to run a query on the field names (not values) in order to select projects related to a given experimental setting (e.g. "time series"), or to a particular field (e.g. "disease type").

Usage

selectProjectsByCharacteristics(
  recount.metadata,
  query.charact,
  run.kable = FALSE,
  run.barplot = FALSE
)

Arguments

recount.metadata	a data.frame containing the metadata, as returned by recount::all_metadata() function.
query.charact	a string indicating the query to be matched against field names in the characteristics tables.
run.kable=FALSE	if TRUE, print out the summary of the matches in kable format for markdown report.
run.barplot=FALSE	if TRUE, draw a barplot with the number of runs per selected project

Author(s)

Mustafa AbuElQumsan and Jacques van Helden

Examples

## Load recount metadata
library(recount)
recount.metadata <- all_metadata(subset='sra')

## Select all the projects having "disease status" as a characteristics field
selectProjectsByCharacteristics(recount.metadata,
   query.charact = "disease status",
   run.barplot = TRUE)

elqumsan/RNAseqMVA documentation built on March 10, 2021, 8:10 a.m.