TIGER batch correction
bc_tiger.RdThis function returns a pmart object that has been undergone TIGER batch effect correction
Usage
bc_tiger(
omicsData,
sampletype_cname,
test_val,
group_cname,
position_cname = NULL,
injection_cname = NULL
)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$f_data that contains the sample type information (such as quality control samples)
- test_val
character string giving the name of the value within the column sampletype_cname to be used as the testing value for TIGER
- group_cname
character string giving the name of the column in omicsData$f_data that contians the group information
- position_cname
character string giving the name of the column in omicsData$f_data that contains the well position, default is NULL
- injection_cname
character string giving the name of the column in omicsData$f_data that contains the injection order, default is NULL
Examples
library(malbacR)
library(pmartR)
data("pmart_amide")
pmart_amide <- group_designation(pmart_amide,main_effects = "group",batch_id = "batch")
tigerFilt <- tiger_filter(pmart_amide,sampletype_cname = "group",test_val = "QC")
pmart_amideFilt <- apply_tigerFilt(tigerFilt,pmart_amide)
#> There are no molecules that need to be removed. Returning the original omicsData
amide_tiger <- bc_tiger(omicsData = pmart_amideFilt,sampletype_cname = "group",
test_val = "QC",injection_cname = "Injection_order",group_cname = "group")
#> + Initialising... 2024-02-06 12:20:01
#> + Computing target values... 2024-02-06 12:20:01
#> + Selecting highly-correlated variables... 2024-02-06 12:20:01
#> - Computing correlation coefficients...
#> - Selecting variables...
#> + Data correction started. 2024-02-06 12:20:02
#>
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#> - Merging results...
#> + Completed. 2024-02-06 12:23:17