Description Usage Arguments Author(s) Examples
View source: R/select_projects_by_characteristics.R
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").
1 2 3 4 5 6 | selectProjectsByCharacteristics(
recount.metadata,
query.charact,
run.kable = FALSE,
run.barplot = FALSE
)
|
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 |
Mustafa AbuElQumsan and Jacques van Helden
1 2 3 4 5 6 7 8 | ## 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)
|
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