TIGER filtering
tiger_filter.RdThis function returns a object of class 'tigerFilt' that has been filtered to ensure TIGER batch correction can run successfully
Arguments
- omicsData
an object of the class 'pepData', 'proData', 'metabData', 'lipidData', or 'nmrData', usually created by
as.pepData,as.proData,as.metabData,as.lipidData, oras.nmrData, respectively.- sampletype_cname
character string giving the name of the column in omicsData$f_data that contains the sample type information (such as quality control samples)
- test_val
character string giving the name of the value within the column sampletype_cname to be used as the testing value for TIGER
Examples
library(malbacR)
library(pmartR)
data(pmart_amide)
pmart_amide <- group_designation(pmart_amide,main_effects = "group",batch_id = "batch")
tigerFilt <- tiger_filter(omicsData = pmart_amide,sampletype_cname = "group", test_val = "QC")
pmart_amide_filt <- apply_tigerFilt(filter_object = tigerFilt,omicsData = pmart_amide)
#> There are no molecules that need to be removed. Returning the original omicsData
amide_tiger <- bc_tiger(omicsData = pmart_amide_filt, sampletype_cname = "group", test_val = "QC",group_cname = "group")
#> + Initialising... 2024-02-06 12:26:22
#> + Computing target values... 2024-02-06 12:26:22
#> + Selecting highly-correlated variables... 2024-02-06 12:26:22
#> - Computing correlation coefficients...
#> - Selecting variables...
#> + Data correction started. 2024-02-06 12:26:23
#>
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#> - Merging results...
#> + Completed. 2024-02-06 12:29:26