merge_input: Uses output from select_regions() to merge output before...

In leekgroup/phenopredict: Predicting phenotypes from RNA-seq expression data

Description

This function takes the output from multiple executions of select_regions() and merges the output before building and running the predictor. Objects output are the merged output from select_regions but contain the same objects.

Usage

merge_input(inputdata_list = NULL)

Arguments

inputdata_list

list out output objects from select_regions() inputdata_list

Value

merged inputdata across multiple runs of select_regions()

Examples

library('GenomicRanges')
library('dplyr')
## make up some expression data for 9 rows and 30 people
data(sysdata, package='phenopredict')
## includes R object 'cm'

## Make up some some region data
regions <- GRanges(seqnames = 'chr2', IRanges(
      start = c(28971710:28971712, 29555081:29555083, 29754982:29754984),
      end = c(29462417:29462419, 29923338:29923340, 29917714:29917716)))

## make up some expression data for 9 rows and 30 people
exp= cm[1:length(regions),1:30]

## Generate first object to be merged
inputdata1 <- list()
inputdata1$covmat = exp
inputdata1$regiondata = regions

## Generate scond object to be merged
regions2 = GRanges(seqnames = 'chr9', IRanges(
      start = c(28971710:28971712, 29555081:29555083, 29754982:29754984),
      end = c(29462417:29462419, 29923338:29923340, 29917714:29917716)))
exp2 = cm[1:length(regions2),1:30]
inputdata2 <- list()
inputdata2$covmat = exp2
inputdata2$regiondata = regions2

## merge objects
inputdata_merged<-merge_input(inputdata_list=list(inputdata1, inputdata2))

leekgroup/phenopredict documentation built on May 14, 2019, 11:27 a.m.