Hello Jianhong Ou,

Thank you very much for your advice, I'm quite new on R and still make such
basic mistakes...

With best wishes

JL

2012/12/3 Ou, Jianhong <Jianhong.Ou@umassmed.edu>

> Hi Dr. Jose,
>
> The parameter data.BED should be an object of data.frame but not a file
> name. You could try:
>
> macs.peaks.bed <- read.delim("macs_peaks.BED", header=FALSE)
> BED2RangedData(macs.peaks.bed)
>
> Yours sincerely,
>
> Jianhong Ou
>
> jianhong.ou@umassmed.edu
>
>
> On Dec 3, 2012, at 3:57 AM, José Luis Lavín wrote:
>
> > Dear list,
> >
> > I'm inteterested on using the bioconductor package ChIPpeakAnno to
> analyze
> > some ChIP-seq experiments. The Vignette of the package describes a series
> > of capabilities that fit perfectly to what I intend to do for my
> analysis.
> > But there's a major prblem with it, when I try to load the BED files I
> > retrieved from peak calling programs such as MACS or SISSRS, I can't.
> > I used BED2RangedData to upload my files but I keep getting the same
> error,
> > e.g.
> >
> > "> BED2RangedData("macs_peaks.BED",header=FALSE)
> >
> > Error in BED2RangedData("macs_peaks.BED", header = FALSE) :
> > No valid data.BED passed in, which is a data frame as BED format file
> with
> > at least 3 fields in the order of: chromosome, start and end. Optional
> > fields are name, score and strand etc. Please refer to
> > http://genome.ucsc.edu/FAQ/FAQformat#format1 for details."
> >
> > I revised the UCSC format page and revised my BED files. To my surprise
> > each so called BED file has a different format, but (at least to my
> > understanding) should comply to BED2RangedData fields
> requitrements...here
> > are my BED files first lines.
> >
> > 1) head macs_peaks.BED
> >
> > chr1    78570032        78571272        MACS_peak_1     64.10
> > chr1    172993763       172996043       MACS_peak_2     79.98
> > chr1    173009505       173012053       MACS_peak_3     113.45
> > chr1    189432746       189433727       MACS_peak_4     55.42
> > chr10   129172524       129172778       MACS_peak_5     70.83
> > chr11   16562386        16562670        MACS_peak_6     53.89
> > chr11   33101311        33101810        MACS_peak_7     53.01
> > chr11   33654680        33655228        MACS_peak_8     51.42
> > chr11   95817226        95817470        MACS_peak_9     53.89
> > chr11   108872843       108873542       MACS_peak_10    69.06
> >
> > 2) head Chip_K27.BED
> >
> > chr5    42860311        42860361
> > HSCAN:310:C1B3LACXX:7:1101:1598:1930    255     +
> > chr7    104626327       104626377
> > HSCAN:310:C1B3LACXX:7:1101:1180:1956    255     +
> > chr7    121488942       121488992
> > HSCAN:310:C1B3LACXX:7:1101:1294:1940    255     +
> > chr2    98507295        98507345
> > HSCAN:310:C1B3LACXX:7:1101:1044:1946    255     +
> > chr18   18078895        18078945
> > HSCAN:310:C1B3LACXX:7:1101:1908:1990    255     -
> > chr8    91855040        91855090
> > HSCAN:310:C1B3LACXX:7:1101:2369:1954    255     +
> > chr11   40921952        40922002
> > HSCAN:310:C1B3LACXX:7:1101:1988:1997    255     +
> > chr17   44823557        44823607
> > HSCAN:310:C1B3LACXX:7:1101:2980:1948    255     +
> > chr2    162682448       162682498
> > HSCAN:310:C1B3LACXX:7:1101:2818:1989    255     +
> > chr9    3003254          3003304
> > HSCAN:310:C1B3LACXX:7:1101:1557:1996    255     +
> >
> > Could anyone help me with this issue, because I really don's understand
> > whats going on here.
> >
> > Thanks in advance
> >
> > JL
> >
> >> sessionInfo()
> > R version 2.15.1 (2012-06-22)
> > Platform: x86_64-redhat-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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=C                 LC_NAME=C
> > [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] grid      stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> > [1] ChIPpeakAnno_2.6.0                  limma_3.14.3
> > [3] org.Hs.eg.db_2.8.0                  GO.db_2.8.0
> > [5] RSQLite_0.11.2                      DBI_0.2-5
> > [7] AnnotationDbi_1.20.3
>  BSgenome.Ecoli.NCBI.20080805_1.3.17
> > [9] BSgenome_1.26.1                     GenomicRanges_1.10.2
> > [11] Biostrings_2.26.2                   IRanges_1.16.2
> > [13] multtest_2.14.0                     Biobase_2.18.0
> > [15] biomaRt_2.14.0                      BiocGenerics_0.4.0
> > [17] VennDiagram_1.5.1                   BiocInstaller_1.8.3
> >
> > loaded via a namespace (and not attached):
> > [1] MASS_7.3-22      parallel_2.15.1  RCurl_1.95-1.1   splines_2.15.1
> > [5] stats4_2.15.1    survival_2.36-14 tools_2.15.1     XML_3.95-0.1
> >
> >
> > --
> > --
> > Dr. José Luis Lavín Trueba
> >
> > Dpto. de Producción Agraria
> > Grupo de Genética y Microbiología
> > Universidad Pública de Navarra
> > 31006 Pamplona
> > Navarra
> > SPAIN
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
-- 
Dr. José Luis Lavín Trueba

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN

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