Dear all,

I am newby in analysing chip-seq data and I am getting an error in coverting
my readaligned object to a GenomeData object

the commands that I am using are:
library(ShortRead)
library(PICS)
library(ChIPpeakAnno)
library(snowfall)
exDir<-("/RAID/Paula_chip_seq_data/")

dataIP_JKA<-readAligned(dirPath=exDir, type="Bowtie",
pattern="110402_SN365_B_s_2_seq_GQG-1")
dataIP_JKA <- as(dataIP_JKA, "GenomeData")

Error in as.list.default(from) :
  no method for coercing this S4 class to a vector
In addition: Warning message:
Storing reads only by their start positions is deprecated. Please use a
range representation like GRanges.
> dataCont_JKA
class: AlignedRead
length: 6443227 reads; width: 50 cycles
chromosome: chr20 chr17 ... chr8 chr21
position: 41162388 77764636 ... 59583233 34102674
strand: - - ... - +
alignQuality: NumericQuality
alignData varLabels: similar mismatch


I  am getting also an error when trying to convert the map file into a
RangeData object

map<-read.table("/RAID/Paula_chip_seq_data/hg19.fa-50.bed", header =
TRUE,colClasses = c("factor", "integer", "integer", "NULL"))
> map <- as(map, "RangedData")

thanks for the help.
Andreia



sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
 [1] snowfall_1.84                       snow_0.3-5
 [3] ChIPpeakAnno_1.8.0                  limma_3.8.2
 [5] org.Hs.eg.db_2.5.0                  GO.db_2.4.1
 [7] RSQLite_0.9-1                       DBI_0.2-5
 [9] AnnotationDbi_1.14.1                BSgenome.Ecoli.NCBI.20080805_1.3.17
[11] multtest_2.8.0                      Biobase_2.12.2
[13] biomaRt_2.8.1                       PICS_1.6.0
[15] BSgenome_1.20.0                     ShortRead_1.10.4
[17] Rsamtools_1.4.2                     lattice_0.19-30
[19] Biostrings_2.20.1                   GenomicRanges_1.4.6
[21] IRanges_1.10.4

loaded via a namespace (and not attached):
[1] grid_2.13.1     hwriter_1.2     MASS_7.3-13     RCurl_1.4-2
[5] splines_2.13.1  survival_2.36-9 XML_3.1-0





-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

	[[alternative HTML version deleted]]

