addDatabase: Intersect correlations with an external database.

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

For each miRNA-mRNA pair, add if this pair has been predicted as miRNA-mRNA interaction according to the desired external databases.

Usage

addDatabase(obj, database, pval.ref=1, dat.sum=1)

Arguments

obj	a corObject with a cytofile slot already defined.
database	"microCosm_v5_18_numeric"; or a character vector including: "microCosm_v5_18", "targetScan_v6.2_18", "PITA_v6_11_TOP", "miRDB_v5.0_21", "miRSVR_aug10_17", "targetScan_v7.0_21", "miRDB_v5.0_21_mouse", "miRSVR_aug10_15_mouse"; or a character with the name of the data.frame containing the database.
pval.ref	only for "microCosm_v5_18_numeric": p value to set if no information is given. Default: 1.
dat.sum	only if "microCosm_v5_18_numeric" is not selected. For future purposes, the minimun number of concurrences across databases that determine that a miRNA-mRNA pair is bioinformatically predicted. By default: 1.

Value

A corObject with new columns added to the net slot. The name and content of the column is dependent on the database selected:

• microCosm_v5_18_numeric: pval.database: p value of the microCosm database. If there is no p value in the database, then the value pval.ref is assigned

• A character vector including the names of the databases: the following columns are created:

  • For each database: column called "dat.xxx", where "xxx" is the name of the database. The values are "0" (no target) or "1" (target).

  • A column called "dat.sum" that is, for each row, the sum of the values of all "dat.xxx" columns.

Note

If the database is a customised data.frame, the row names must follow the format "miRNA_name:mRNA_name" (check head(microCosm_v5_18) or head(targetScan_v6.2_18)). MiRNA names of the corObject and the database must be of the same miRBase version. See \link{translatemiRNAs} for more detials

References

TargetScan: http://www.targetscan.org/ MicroCosm: http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ MiRDB: http://mirdb.org/ MiRSVR: http://www.microrna.org/microrna/home.do MiRBase: http://www.mirbase.org/

See Also

data(microCosm_v5_18), data(targetScan_v6.2_18), addNet, translatemiRNAs

Examples

## load databases
data(microCosm_v5_18)
data(targetScan_v6.2_18)

## load corObject example
data(data.obj)

## numeric example
data.obj.datadded.numeric <- addDatabase(data.obj, "microCosm_v5_18_numeric")
head(data.obj.datadded.numeric@net)

## non-numeric example, multiple databases
data.obj.datadded.multiple <- addDatabase(data.obj,
 c("microCosm_v5_18", "targetScan_v6.2_18"))
head(data.obj.datadded.multiple@net)

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.