Accessor semData slot in a SEMplScores object
Source:R/AllGenerics.R, R/methods-SEMplScores.R, R/methods-SNPEffectMatrixCollection.R
semData.RdAccessor semData slot in a SEMplScores object
Access semData from a SNPEffectMatrixCollection object
Usage
semData(x)
# S4 method for class 'SEMplScores'
semData(x)
# S4 method for class 'SNPEffectMatrixCollection'
semData(x)Examples
library(VariantAnnotation)
# load default SEMs
data(SEMC)
# create a VRanges object
vr <- VRanges(
seqnames = "chr12",
ranges = 94136009,
ref = "G", alt = "C"
)
# calculate binding propensity
s <- scoreVariants(vr, SEMC, BSgenome.Hsapiens.UCSC.hg19::Hsapiens)
semData(s)
#> Key: <transcription_factor>
#> transcription_factor ensembl_id
#> <char> <char>
#> 1: AHR ENSG00000106546
#> 2: AHR:ARNT:HIF1A ENSG00000106546;ENSG00000143437;ENSG00000100644
#> 3: ARID3A ENSG00000116017
#> 4: ARNT ENSG00000143437
#> 5: ARNTL ENSG00000133794
#> ---
#> 219: ZFX ENSG00000005889
#> 220: ZNF18 ENSG00000154957
#> 221: ZNF217 ENSG00000171940
#> 222: ZNF281 ENSG00000162702
#> 223: ZSCAN4 ENSG00000180532
#> ebi_complex_ac uniprot_ac PWM_id
#> <char> <char> <char>
#> 1: P35869 M00778
#> 2: P35869;P27540;Q16665 M00976
#> 3: Q99856 MA0151.1
#> 4: P27540 ARNT_HUMAN.H11MO.0.B
#> 5: O00327 BMAL1_HUMAN.H11MO.0.A
#> ---
#> 219: P17010 ZFX_HUMAN.H11MO.0.A
#> 220: P17022 ZNF18_HUMAN.H11MO.0.C
#> 221: O75362 M01306
#> 222: Q9Y2X9 ZN281_HUMAN.H11MO.0.A
#> 223: Q8NAM6 Zscan4_pwm_secondary
#> SEM SEM_baseline cell_type neg_log10_pval
#> <char> <num> <char> <num>
#> 1: M00778.sem -0.6717610 HepG2 18.350950
#> 2: M00976.sem -0.5938010 HepG2 14.290190
#> 3: MA0151.1.sem -0.4020880 HepG2 2.980258
#> 4: ARNT_HUMAN.GM12878.sem -1.8632604 GM12878 12.081160
#> 5: BMAL1_HUMAN.HepG2.sem -1.5977194 HepG2 20.220840
#> ---
#> 219: ZFX_HUMAN.HepG2.sem -0.2478717 HepG2 3.443155
#> 220: ZNF18_HUMAN.HEK293.sem -1.6459529 HEK293 3.793244
#> 221: M01306.sem -0.4596240 GM12878 2.843803
#> 222: ZN281_HUMAN.HepG2.sem -0.3926150 HepG2 3.428189
#> 223: ZSCAN4_secondary.sem -2.9110180 HEK293 11.973690
#> chip_ENCODE_accession dnase_ENCODE_accession PWM_source
#> <char> <char> <char>
#> 1: ENCFF242PUG ENCFF001UVU TRANSFAC
#> 2: ENCFF242PUG ENCFF001UVU TRANSFAC
#> 3: ENCFF460WFF ENCFF001UVU JASPAR
#> 4: ENCFF538DNI ENCFF759OLD HOCOMOCOv11
#> 5: ENCFF363NHH ENCFF897NME HOCOMOCOv11
#> ---
#> 219: ENCFF329DCV ENCFF897NME HOCOMOCOv11
#> 220: ENCFF888BHA ENCFF285OXK HOCOMOCOv11
#> 221: ENCFF807UJN ENCFF097LEF TRANSFAC
#> 222: ENCFF948PYK ENCFF897NME HOCOMOCOv11
#> 223: ENCFF485WHZ ENCFF910QHN UNIPROBE
## Create example SEM
df <- data.frame(
A = c(1, 2, 3),
C = c(1, 2, 3),
G = c(1, 2, 3),
T = c(1, 2, 3)
)
sem_data <- data.frame(SEM = "motif_id", TF = "tf_id")
s <- SNPEffectMatrix(df, 1.205, "motif_id")
sc <- SNPEffectMatrixCollection(s, semData = sem_data, semKey = "SEM")
## Access count matrix
semData(sc)
#> Key: <SEM>
#> SEM TF
#> <char> <char>
#> 1: motif_id tf_id