[BioC] ChIPpeakAnno annotatePeakInBatch error message

[Dario Strbenac]

Hello,

I made another small example of using annoPeakInBatch to demonstrate to a friend, but it has crashed. It's similar to the other example but with different data. I'm not sure why it is happening.

Here is my small example:

peaksT <- data.frame(chr = c("chr1", "chr1", "chr1", "chr2", "chr2", "chr2"), start = c(2000010, 19000000, 30000000, 300, 5500, 100000), end = c(2000310, 19000300, 30000300, 600, 5800, 100300))
featuresT <- data.frame(name = c("gene1", "gene2", "gene3", "gene4", "gene5", "gene6"), chr = c("chr1", "chr1", "chr1", "chr2", "chr2", "chr2"), start = c(1000000, 10000000, 15000000, 1000, 6000, 10000), end = c(2000000, 20000000, 22000000, 5000, 7000, 15000), strand = c('+', '-', '+', '+', '-', '+'))

require(ChIPpeakAnno)
	
peaksRangedData <- RangedData(space = peaksT$chr, ranges = IRanges(start = peaksT$start, end = peaksT$end))
featuresRangedData <- RangedData(name = featuresT$name, space = featuresT$chr, strand = featuresT$strand, ranges = IRanges(start = featuresT$start, end = featuresT$end))
featureLoc <- "TSS"

annotatePeakInBatch(peaksRangedData, AnnotationData = featuresRangedData, PeakLocForDistance = "middle")

Error in if (as.character(r.n$strand[i]) == "1" || as.character(r.n$strand[i]) ==  : 
  missing value where TRUE/FALSE needed

My sessionInfo is :

R version 2.11.0 (2010-04-22) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ChIPpeakAnno_1.5.2                  limma_3.4.0                        
 [3] org.Hs.eg.db_2.4.1                  GO.db_2.4.1                        
 [5] RSQLite_0.9-0                       DBI_0.2-5                          
 [7] AnnotationDbi_1.10.0                BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.16.1                     GenomicRanges_1.0.1                
[11] Biostrings_2.16.0                   IRanges_1.6.2                      
[13] multtest_2.4.0                      Biobase_2.8.0                      
[15] biomaRt_2.4.0                      

loaded via a namespace (and not attached):
[1] MASS_7.3-6      RCurl_1.4-2     splines_2.11.0  survival_2.35-8
[5] XML_3.1-0      


Thanks,
       Dario.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia