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Check Res Obj Instruction

Source: vignettes/instruction_checkResObj.Rmd
instruction_checkResObj.Rmd

instruction for Res Obj check

Xiangming Cai

2026-01-28

🔍 Introduction

The ResObj Object contains all relavant informations. If you are interested, please read our paper (mentioned on the top) to know the concepts of each matrix shown here. See CreateRes and SlopEstimation for detailed introduction of the structure of ResObj.

💻 Installation

You can install the development version of USERM from GitHub with:

devtools::install_github("xiangmingcai/USERM")

Step 1 📈 query avalilable fluorescence list

You can use querySig function to query all available fluorescence.

library(USERM)
Sig_info = querySig()
head(Sig_info)
> head(Sig_info)
                    id PrimaryName SecondaryName detectors instrument       Source Note
1  SCC_Bead_CD4_NFR700         CD4        NFR700        51     Xenith XiangmingCai   NA
2   SCC_Bead_CD3_BV510         CD3         BV510        51     Xenith XiangmingCai   NA
3    SCC_Bead_CD2_FITC         CD2          FITC        51     Xenith XiangmingCai   NA
4       SCC_Bead_AF_AF          AF            AF        51     Xenith XiangmingCai   NA
5   SCC_Bead_CD8_BV570         CD8         BV570        51     Xenith XiangmingCai   NA
6 SCC_Bead_CD16_BUV805        CD16        BUV805        51     Xenith XiangmingCai   NA

To check signature of a specific fluroescence, you may

fluor_to_check = Sig_info$id[3]
print(fluor_to_check)
checkSig_linePlot(id = fluor_to_check)
> print(fluor_to_check)
[1] "SCC_Bead_CD2_FITC"

These available fluorescence were preprocessed with parameters extracted for residual model. To access the corresponding residaul model and its parameters, you can use the getRes function.

ResObj = getRes(id = fluor_to_check)

You can easily visaulize all these matrixes, when you are interested in any one of them.

To check the slop matrix:

checkRes_slopMtx(Res = ResObj)

To check the intercept matrix:

checkRes_interceptMtx(Res = ResObj)

You can check the covariance matrix at a specified fluorescence intensity (bin):

print(ResObj$bin_mids)
checkRes_covMtx(Res = ResObj,bin=3)

You can even check the linear fitting of covariance versus fluorescence intensity (bin) between two speific detectors:

print(ResObj$detectors)
checkRes_covScatter(Res = ResObj,
                    detector1 = ResObj$detectors[1],
                    detector2 = ResObj$detectors[2])