inst/examples/transform_chromatoplots_output.R

In mariev/chromatoplotsgui: Interactive graphics and interface for chromatoplots

## transform the data objects from /examples/mac_calibrated.R to generic class objects that don't rely on commandr
## or chromatoplots


load('data/processed/mac_control_step1_4.rda')
load('data/processed/mac_loadSample_calibrated.rda')

chromData <- c(paste('raw', 1:9, sep = ''), 'raw_prof1', 'cor_prof1')
chromData_list <- lapply(chromData, FUN = function(x){
    return(.transform(get(x)))
    
})

names(chromData_list) <- chromData

chromData_xcms <- sapply(chromData, FUN = function(x){print(.reduce(get(x)))})

# save(chromData_list, file = 'data/processed/chromData_list.rda')
# save(chromData_xcms, file = 'data/processed/chromData_xcms.rda')

load('data/processed/mac_step5.rda')
load('data/processed/mac_step6.rda')
load('data/processed/mac_step7_11.rda')
ci_expList <- .transform(ci_exp)
xset_compsList <- .transform(xset_comps)
xset_groupsList <- .transform(xset_groups)
xset_rtcorList <-.transform(xset_rtcor)
xset_groups2List <-.transform(xset_groups2)
xset_sumList <-.transform(xset_sum)
xset_normList <- .transform(xset_norm)

ci_expXCMS <- .reduce(ci_exp)
xset_compsXCMS <- .reduce(xset_comps)
xset_groupsXCMS <- .reduce(xset_groups)
xset_rtcorXCMS <-.reduce(xset_rtcor)
xset_groups2XCMS <-.reduce(xset_groups2)
xset_sumXCMS <-.reduce(xset_sum)
xset_normXCMS <- .reduce(xset_norm)

# save(ci_expList, xset_compsList, xset_groupsList, xset_rtcorList, 
# xset_groups2List, xset_sumList, xset_normList, file = 'chromData_part2.rda')

# save(ci_expXCMS, xset_compsXCMS, xset_groupsXCMS, xset_rtcorXCMS, 
# xset_groups2XCMS, xset_sumXCMS, xset_normXCMS, file = 'data/processed/chromDataXCMS_part2.rda')