Dear expert,
I am using crlmm and VanillaICE for copy number inference with human660quadv1. I have try follow code, but I get a error and warnings.
library("crlmm")
library("VanillaICE")
library(ff)
ocProbesets(150e3)
ocSamples(500)
samplesheet <- cbind(phenotype,paste(phenotype[,2],phenotype[,3],sep="_"))
colnames(samplesheet) <- c("samplename","SentrixBarcode_A","SentrixPosition_A","filename")
batch <- factor(rep("b",nrow(samplesheet)))
arrayInfo <- list(barcode=NULL, position="SentrixPosition")
arrayNames <- file.path(datdir,samplesheet[, "filename"])
gensnp <- genotype.Illumina(sampleSheet=samplesheet,
arrayNames=arrayNames,
copynumber = T,
arrayInfoColNames=arrayInfo,
cdfName="human660quadv1a",
batch=batch,
verbose=T)
library(oligoClasses)
library(VanillaICE)
library(crlmm)
library(SNPchip)
library(IRanges)
library(foreach)
registerDoSEQ()
se <- as(gensnp, "SnpArrayExperiment")
#library(ArrayTV)
#i <- seq_len(ncol(se))
#increms <- c(10,1000,100e3)
#wins <- c(100,10e3,1e6)
#res <- gcCorrect(lrr(se),
# increms=increms,
# maxwins=wins,
# returnOnlyTV=FALSE,
# verbose=TRUE,
# build="hg18",
# chr=chromosome(se),
# starts=start(se))
#se2 <- se
#assays(se2)[["cn"]] <- res$correctedVals
res <- hmm2(se2)
filter_param <- FilterParam()
show(filter_param)
cnvFilter(res, filter_param)
select_cnv <- FilterParam(state=c("1", "2", "5", "6"), seqnames="chr22")
cnvs <- cnvFilter(res, select_cnv)
cnvs
The warning is from : se <- as(gensnp, "SnpArrayExperiment")
se <- as(gensnp, "SnpArrayExperiment")
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There were 24 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In calculateRBafCNSet(object, batch.name, chrom) :
Only computing log R ratios and BAFs for autosomes and chr X
2: In integerMatrix(lrr, 100) : NAs introduced by coercion
3: In integerMatrix(lrr, 100) : NAs introduced by coercion
4: In integerMatrix(lrr, 100) : NAs introduced by coercion
The error is:
> res <- hmm2(se)
Error in { :
task 1 failed - "error in evaluating the argument 'x' in selecting a method for function 'NA_filter': Error in `[.ff`(list(), 1L, drop = FALSE) :
unused argument (drop = FALSE)
"