eqtl using ggtools
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2.8 years ago
archie ▴ 120

Hi everyone

I am trying to run GGtools for prediction of eqtl based on the genotypes and expression information. https://bioconductor.org/packages/release/bioc/vignettes/GGtools/inst/doc/GGtools.pdf

I am trying to run function gwSnpTests which needs the exxpression object and phontype information

step 1

es = new("ExpressionSet", exprs=exprs1,phenoData=phenoData,featureData = fdata)

Expressionset variable (es)

ExpressionSet (storageMode: lockedEnvironment) assayData: 55 features, 19 samples element names: exprs protocolData: none phenoData sampleNames: F545 F546 ... F563 (19 total) varLabels: ID S Ph varMetadata: labelDescription featureData featureNames: AC090958.3 CR847794.2 ... MIR4774 (55 total) fvarLabels: GeneID fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation:

step 2

ss = make_smlSet(es, list("1" =xx$genotypes) ,annotation(es))

smlset variable (ss)

SnpMatrix-based genotype set: number of samples: 19 number of chromosomes present: 1 annotation:
Expression data dims: 14000 x 19 Total number of SNP: 4500 Phenodata: An object of class 'AnnotatedDataFrame' sampleNames: F545 F546 ... F563 (19 total) varLabels: ID S Ph varMetadata: labelDescription

step 3.

I am using the fvarLabels: genesym, also present in my expressionset fdata.

t1 = gwSnpTests(genesym("sym")~S , ss)

character(0) Failed with error: ‘'package' must be of length 1’ Error in revmap(get(paste(gsub(".db", "", annpack), "SYMBOL", sep = ""))) : error in evaluating the argument 'x' in selecting a method for function 'revmap': Error in get(paste(gsub(".db", "", annpack), "SYMBOL", sep = "")) : object 'SYMBOL' not found

How to define and create the instances genesym to run function gwSnpTests

I am stuck at this step. Please help me to sort this issue.

I will appreciate all the suggestion.

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