The NanoStringGeomxSet was inherited from Biobase’s ExpressionSet class. The NanoStringGeomxSet class was designed to encapsulate data and corresponding methods for NanoString DCC files generated from the NanoString GeoMx Digital Spatial Profiling (DSP) platform.
Loading the NanoStringNCTools and GeomxTools packages allow users access to the GeomxSet class and corresponding methods.
datadir <- system.file("extdata", "DSP_NGS_Example_Data",
package="GeomxTools")
DCCFiles <- dir(datadir, pattern=".dcc$", full.names=TRUE)
PKCFiles <- unzip(zipfile = file.path(datadir, "/pkcs.zip"))
SampleAnnotationFile <- file.path(datadir, "annotations.xlsx")
demoData <-
suppressWarnings(readNanoStringGeomxSet(dccFiles = DCCFiles,
pkcFiles = PKCFiles,
phenoDataFile = SampleAnnotationFile,
phenoDataSheet = "CW005",
phenoDataDccColName = "Sample_ID",
protocolDataColNames = c("aoi",
"cell_line",
"roi_rep",
"pool_rep",
"slide_rep"),
experimentDataColNames = c("panel")))
class( demoData )
#> [1] "NanoStringGeomxSet"
#> attr(,"package")
#> [1] "GeomxTools"
isS4( demoData )
#> [1] TRUE
is( demoData, "ExpressionSet" )
#> [1] TRUE
demoData
#> NanoStringGeomxSet (storageMode: lockedEnvironment)
#> assayData: 1821 features, 89 samples
#> element names: exprs
#> protocolData
#> sampleNames: DSP-1001250002642-A01.dcc DSP-1001250002642-A02.dcc ...
#> DSP-1001250002642-H05.dcc (89 total)
#> varLabels: FileVersion SoftwareVersion ... slide_rep (24 total)
#> varMetadata: labelDescription
#> phenoData
#> sampleNames: DSP-1001250002642-A01.dcc DSP-1001250002642-A02.dcc ...
#> DSP-1001250002642-H05.dcc (89 total)
#> varLabels: slide name scan name ... area (5 total)
#> varMetadata: labelDescription
#> featureData
#> featureNames: A2M ABCB1 ... ZNF207 (1821 total)
#> fvarLabels: Gene
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation: Six-gene_test_v1_v1.1.pkc VnV_GeoMx_Hs_CTA_v1.2.pkc
#> signature: noneAlongside the accessors associated with the ExpressionSet class, NanoStringGeomxSet objects have unique additional assignment and accessor methods faciliting common ways to view DSP data and associated labels.
head( pData( demoData ), 2 )
#> slide name
#> DSP-1001250002642-A01.dcc No Template Control
#> DSP-1001250002642-A02.dcc 6panel-old-slide1 (PTL-10891)
#> scan name roi segment
#> DSP-1001250002642-A01.dcc <NA> NA <NA>
#> DSP-1001250002642-A02.dcc cw005 (PTL-10891) Slide1 1 Geometric Segment
#> area
#> DSP-1001250002642-A01.dcc NA
#> DSP-1001250002642-A02.dcc 31318.73
protocolData( demoData )
#> An object of class 'AnnotatedDataFrame'
#> sampleNames: DSP-1001250002642-A01.dcc DSP-1001250002642-A02.dcc ...
#> DSP-1001250002642-H05.dcc (89 total)
#> varLabels: FileVersion SoftwareVersion ... slide_rep (24 total)
#> varMetadata: labelDescription
svarLabels( demoData )
#> [1] "slide name" "scan name" "roi" "segment"
#> [5] "area" "FileVersion" "SoftwareVersion" "Date"
#> [9] "ID" "Plate_ID" "Well" "SeqSetId"
#> [13] "tamperedIni" "trimGaloreOpts" "flash2Opts" "umiExtractOpts"
#> [17] "bowtie2Opts" "umiDedupOpts" "Raw" "Trimmed"
#> [21] "Stitched" "Aligned" "umiQ30" "rtsQ30"
#> [25] "aoi" "cell_line" "roi_rep" "pool_rep"
#> [29] "slide_rep"
head( sData(demoData), 2 )
#> slide name
#> DSP-1001250002642-A01.dcc No Template Control
#> DSP-1001250002642-A02.dcc 6panel-old-slide1 (PTL-10891)
#> scan name roi segment
#> DSP-1001250002642-A01.dcc <NA> NA <NA>
#> DSP-1001250002642-A02.dcc cw005 (PTL-10891) Slide1 1 Geometric Segment
#> area FileVersion SoftwareVersion Date
#> DSP-1001250002642-A01.dcc NA 0.1 1.0.0 2020-07-14
#> DSP-1001250002642-A02.dcc 31318.73 0.1 1.0.0 2020-07-14
#> ID Plate_ID Well
#> DSP-1001250002642-A01.dcc DSP-1001250002642-A01 1001250002642 A01
#> DSP-1001250002642-A02.dcc DSP-1001250002642-A02 1001250002642 A02
#> SeqSetId tamperedIni
#> DSP-1001250002642-A01.dcc VH00121:3:AAAG2YWM5 No
#> DSP-1001250002642-A02.dcc VH00121:3:AAAG2YWM5 No
#> trimGaloreOpts
#> DSP-1001250002642-A01.dcc " --hardtrim5 26 --dont_gzip"
#> DSP-1001250002642-A02.dcc " --hardtrim5 26 --dont_gzip"
#> flash2Opts
#> DSP-1001250002642-A01.dcc " -m 26 -e 26 -f 26 -s 1 -r 27"
#> DSP-1001250002642-A02.dcc " -m 26 -e 26 -f 26 -s 1 -r 27"
#> umiExtractOpts
#> DSP-1001250002642-A01.dcc " --bc-pattern=NNNNNNNNNNNNNN"
#> DSP-1001250002642-A02.dcc " --bc-pattern=NNNNNNNNNNNNNN"
#> bowtie2Opts
#> DSP-1001250002642-A01.dcc " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
#> DSP-1001250002642-A02.dcc " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
#> umiDedupOpts Raw Trimmed
#> DSP-1001250002642-A01.dcc " --edit-distance-threshold=1" 161 161
#> DSP-1001250002642-A02.dcc " --edit-distance-threshold=1" 646250 646250
#> Stitched Aligned umiQ30 rtsQ30
#> DSP-1001250002642-A01.dcc 12 12 0 0
#> DSP-1001250002642-A02.dcc 616150 610390 0 0
#> aoi cell_line roi_rep pool_rep
#> DSP-1001250002642-A01.dcc <NA> <NA> NA NA
#> DSP-1001250002642-A02.dcc Geometric Segment-aoi-001 HS578T 1 1
#> slide_rep
#> DSP-1001250002642-A01.dcc NA
#> DSP-1001250002642-A02.dcc 1Design information can be assigned to the NanoStringGeomxSet object, as well as feature and sample labels to use for NanoStringGeomxSet plotting methods.
design( demoData ) <- ~ `segments`
design( demoData )
#> ~segments
dimLabels( demoData )
#> [1] "GeneName" "SampleID"
dimLabels( demoData )[2] <- "Sample ID"
dimLabels( demoData )
#> [1] "GeneName" "Sample ID"sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.13-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 parallel stats graphics grDevices utils datasets
#> [8] methods base
#>
#> other attached packages:
#> [1] GeomxTools_1.0.0 NanoStringNCTools_1.0.0 ggplot2_3.3.3
#> [4] S4Vectors_0.30.0 Biobase_2.52.0 BiocGenerics_0.38.0
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.6 Biostrings_2.60.0 assertthat_0.2.1
#> [4] digest_0.6.27 utf8_1.2.1 plyr_1.8.6
#> [7] R6_2.5.0 GenomeInfoDb_1.28.0 cellranger_1.1.0
#> [10] evaluate_0.14 pillar_1.6.1 zlibbioc_1.38.0
#> [13] rlang_0.4.11 uuid_0.1-4 readxl_1.3.1
#> [16] jquerylib_0.1.4 rmarkdown_2.8 EnvStats_2.4.0
#> [19] stringr_1.4.0 htmlwidgets_1.5.3 pheatmap_1.0.12
#> [22] RCurl_1.98-1.3 ggiraph_0.7.10 munsell_0.5.0
#> [25] compiler_4.1.0 vipor_0.4.5 xfun_0.23
#> [28] pkgconfig_2.0.3 systemfonts_1.0.2 ggbeeswarm_0.6.0
#> [31] htmltools_0.5.1.1 tidyselect_1.1.1 tibble_3.1.2
#> [34] GenomeInfoDbData_1.2.6 IRanges_2.26.0 fansi_0.4.2
#> [37] crayon_1.4.1 dplyr_1.0.6 withr_2.4.2
#> [40] bitops_1.0-7 grid_4.1.0 jsonlite_1.7.2
#> [43] gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1
#> [46] magrittr_2.0.1 scales_1.1.1 stringi_1.6.2
#> [49] reshape2_1.4.4 XVector_0.32.0 ggthemes_4.2.4
#> [52] bslib_0.2.5.1 ellipsis_0.3.2 generics_0.1.0
#> [55] vctrs_0.3.8 rjson_0.2.20 RColorBrewer_1.1-2
#> [58] tools_4.1.0 glue_1.4.2 beeswarm_0.3.1
#> [61] purrr_0.3.4 yaml_2.2.1 colorspace_2.0-1
#> [64] knitr_1.33 sass_0.4.0