beadarrayMSV (version 1.1.0)

BSRed.193: Atlantic salmon genotype data with mainly MSV-5 markers

Description

This data set contains data for 193 markers genotyped for 3230 Atlantic salmon half-sib family individuals. A large part of the markers are multisite variants segregating in both paralogs (MSV-5's)

Usage

data(BSRed.193)

Format

The format is: Formal class 'AlleleSetIllumina' [package beadarrayMSV] with 7 slots ..@ assayData : List of 6 .. ..$ intensity : num [1:193, 1:3230] 7.05 6.17 2.94 4.28 4.23 ... .. ..$ theta : num [1:193, 1:3230] 0.3469 0.4952 0.7389 -0.0202 0.3441 ... .. ..$ SE : num [1:193, 1:3230] 0.00582 0.00402 0.01764 0.00941 0.01083 ... .. ..$ call : num [1:193, 1:3230] 0.25 0.75 0.75 0 0.25 1 0.75 0.5 0 0.75 ... .. ..$ ped.check : logi [1:193, 1:3230] TRUE NA TRUE TRUE TRUE TRUE ... .. ..$ ped.check.parents: num [1:193, 1:3230] 0 0 0 0 0 0 0 0 0 0 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:193] "AY388579_a" "AY388580_a" "ESTNV_14208_491" ... .. .. .. ..$ : chr [1:3230] "X4469076125_A" "X4469076125_B" "X4469076309_A" ... ..@ phenoData : Formal class 'AnnotatedDataFrame' [package Biobase] with 4 slots .. .. ..@ varMetadata :'data.frame': 14 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:14] "Array ID" "No. detected beads" "Chip ID" ... .. .. ..@ data :'data.frame': 3230 obs. of 14 variables: .. .. .. ..$ arrayNames : chr [1:3230] "4469076125_A" "4469076125_B" "4469076309_A" ... .. .. .. ..$ no.beads : int [1:3230] 558739 542929 549125 526811 511354 ... .. .. .. ..$ chip : num [1:3230] 4.47e+09 4.47e+09 4.47e+09 4.47e+09 4.47e+09 ... .. .. .. ..$ row : chr [1:3230] "A" "B" "A" "B" ... .. .. .. ..$ col : int [1:3230] 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ noiseIntensity: num [1:3230] 0.995 1.063 0.859 0.89 1.019 ... .. .. .. ..$ Sample.ID : chr [1:3230] "100050151" "100050152" "100050153" ... .. .. .. ..$ Sample.Plate : chr [1:3230] "SMS_009" "SMS_009" "SMS_009" ... .. .. .. ..$ Sample.Name : chr [1:3230] "017_532_0385" "017_532_0386" "017_532_0387" ... .. .. .. ..$ AMP.Plate : chr [1:3230] "WG0011117-MSA2" "WG0011117-MSA2" ... .. .. .. ..$ Sample.Well : chr [1:3230] "E01" "F01" "G01" ... .. .. .. ..$ Parent1 : chr [1:3230] "100000000" "100000000" "100000000" ... .. .. .. ..$ Parent2 : chr [1:3230] "100050100" "100050100" "100050100" ... .. .. .. ..$ PedigreeID : chr [1:3230] "199950151" "199950152" "199950153" ... ..@ featureData : Formal class 'AnnotatedDataFrame' [package Biobase] with 4 slots .. .. ..@ varMetadata :'data.frame': 16 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:16] "" "Marker ID" "Polymorphism" ... .. .. ..@ data :'data.frame': 193 obs. of 16 variables: .. .. .. ..$ Index : int [1:193] 2 3 256 426 640 ... .. .. .. ..$ Name : chr [1:193] "AY388579_a" "AY388580_a" "ESTNV_14208_491" ... .. .. .. ..$ SNP : chr [1:193] "[A/G]" "[T/G]" "[T/C]" ... .. .. .. ..$ ILMN.Strand : chr [1:193] "TOP" "BOT" "BOT" ... .. .. .. ..$ Address : int [1:193] 7560672 6370541 6660563 2190240 3140563 ... .. .. .. ..$ Address2 : int [1:193] 0 0 0 0 0 0 3120064 0 ... .. .. .. ..$ Norm.ID : int [1:193] 1 2 2 2 2 2 102 2 ... .. .. .. ..$ Classification: chr [1:193] "MSV-5" "FAIL" "MSV-5" ... .. .. .. ..$ Cent.Deviation: num [1:193] 0.2315 0.3952 0.0796 0.018 0.0863 ... .. .. .. ..$ Within.SD : num [1:193] 0.0258 0.0176 0.0494 0.0188 0.0332 ... .. .. .. ..$ HW.Chi2 : num [1:193] 0.524 8.113 9.541 NA 7.628 ... .. .. .. ..$ HW.P : num [1:193] 0.9135 0.0437 0.0229 NA 0.0544 ... .. .. .. ..$ BAF.Locus1 : num [1:193] 0.508 0.819 0.887 NA 0.285 ... .. .. .. ..$ BAF.Locus2 : num [1:193] 0.508 0.729 0.359 NA 0.126 ... .. .. .. ..$ Call.Rate : num [1:193] 0.981 0.912 0.95 0.98 0.978 ... .. .. .. ..$ Manual.Calls.R: chr [1:193] "MSV-5" "MSV-5" "MSV-5" ... ..@ experimentData :Formal class 'MIAME' [package Biobase] ..@ annotation : chr(0) ..@ protocolData :Formal class 'AnnotatedDataFrame' [package Biobase] ..@ .__classVersion__:Formal class 'Versions' [package Biobase]

Source

L. Gidskehaug, M. Kent, B. J. Hayes, and S. Lien. (2011) Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP-array. Bioinformatics, 27(3):303-310

Examples

data(BSRed.193)
print(BSRed.193)
varMetadata(BSRed.193)
fvarMetadata(BSRed.193)
assayData(BSRed.193)$call[1:10,1:4]

## Not run: 
# plotGenotypes(BSRed.193,markers=1:12)
# ## End(Not run)