SeSAMe implements inference of sex, age, ethnicity. These are valuable information for checking the integrity of the experiment and detecting sample swaps.

## [1] TRUE

Sex

Sex is inferred based on our curated X-linked probes and Y chromosome probes excluding pseudo-autosomal regions.

## [1] "MALE"
## [1] "XaY"

Ethnicity

Ethnicity is inferred using a random forest model trained based on both the built-in SNPs (rs probes) and channel-switching Type-I probes.

## [1] "WHITE"

Age

SeSAMe provides age regression a la the Horvath 353 model.

## [1] 84.13913

Mean intensity

The mean intensity of all the probes characterize the quantity of input DNA and efficiency of probe hybridization.

## [1] 3155.071

Copy Number

SeSAMe performs copy number variation in three steps: 1) normalizes the signal intensity using a copy-number-normal data set; 2) groups adjacent probes into bins; 3) runs DNAcopy internally to group bins into segments.

To visualize segmentation in SeSAMe,

Cell Composition Deconvolution

SeSAMe estimates leukocyte fraction using a two-component model.This function works for samples whose targeted cell-of-origin is not related to white blood cells.

## [1] 0.2007592

Session Info

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] scales_1.1.1         DNAcopy_1.68.0       GenomicRanges_1.46.1
##  [4] GenomeInfoDb_1.30.1  IRanges_2.28.0       S4Vectors_0.32.3    
##  [7] wheatmap_0.1.0       ggplot2_3.3.5        sesame_1.12.9       
## [10] sesameData_1.12.0    rmarkdown_2.11       ExperimentHub_2.2.1 
## [13] AnnotationHub_3.2.1  BiocFileCache_2.2.1  dbplyr_2.1.1        
## [16] BiocGenerics_0.40.0 
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## loaded via a namespace (and not attached):
##  [1] matrixStats_0.61.0            bitops_1.0-7                 
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##  [5] filelock_1.0.2                httr_1.4.2                   
##  [7] tools_4.1.2                   bslib_0.3.1                  
##  [9] utf8_1.2.2                    R6_2.5.1                     
## [11] KernSmooth_2.23-20            DBI_1.1.2                    
## [13] colorspace_2.0-2              withr_2.4.3                  
## [15] tidyselect_1.1.1              gridExtra_2.3                
## [17] preprocessCore_1.56.0         bit_4.0.4                    
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## [59] plyr_1.8.6                    grid_4.1.2                   
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## [93] AnnotationDbi_1.56.2          memoise_2.0.1                
## [95] ellipsis_0.3.2                interactiveDisplayBase_1.32.0
## [97] BiocStyle_2.22.0