[BioC] Problem loading BED file with BED2RangedData

[Ou, Jianhong]

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 at 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 at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor