Hello, I have a dataframe df1 and a grange object gr. The rownames respectively names (gr) are identical but not necessary in the same order. I wish to append df1 as metadata to the gr (of course rownames (df) and names (gr) must fit). Could you please give me a hint. Thanks Hermann > df1 Strand A1 A2 rs3737728 u C T rs6687776 u C T rs9651273 u G A > gr GRanges with 3 ranges and 1 metadata column: seqnames ranges strand | score <rle> <iranges> <rle> | <character> rs3737728 chr1 [1021415, 1021415] * | 0.340955 rs6687776 chr1 [1030565, 1030565] * | 0.438123 rs9651273 chr1 [1031540, 1031540] * | 0.196662 --- seqlengths: chr1 chr10 ... chrX chrY NA NA ... NA NA > dput (df1) structure(list(Strand = structure(c(1L, 1L, 1L), .Label = "u", class = "factor"), A1 = structure(c(2L, 2L, 3L), .Label = c("A", "C", "G", "T" ), class = "factor"), A2 = structure(c(4L, 4L, 1L), .Label = c("A", "C", "G", "T"), class = "factor")), .Names = c("Strand", "A1", "A2"), class = "data.frame", row.names = c("rs3737728", "rs6687776", "rs9651273")) > dput (gr) new("GRanges" , seqnames = new("Rle" , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") , lengths = 3L , elementMetadata = NULL , metadata = list() ) , ranges = new("IRanges" , start = c(1021415L, 1030565L, 1031540L) , width = c(1L, 1L, 1L) , NAMES = c("rs3737728", "rs6687776", "rs9651273") , elementType = "integer" , elementMetadata = NULL , metadata = list() ) , strand = new("Rle" , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") , lengths = 3L , elementMetadata = NULL , metadata = list() ) , elementMetadata = new("DataFrame" , rownames = NULL , nrows = 3L , listData = structure(list(score = c("0.340955", "0.438123", "0.196662")), .Names = "score") , elementType = "ANY" , elementMetadata = NULL , metadata = list() ) , seqinfo = new("Seqinfo" , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_) , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA) , genome = c("hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19") ) , metadata = list(<s4 object="" of="" class="" structure("dataframe",="" package="IRanges" )="">) ) > [[alternative HTML version deleted]]

On Tue, Jul 16, 2013 at 11:22 AM, Hermann Norpois <hnorpois@gmail.com>wrote: > Hello, > > I have a dataframe df1 and a grange object gr. The rownames respectively > names (gr) are identical but not necessary in the same order. I wish to > append df1 as metadata to the gr (of course rownames (df) and names (gr) > must fit). > > Could you please give me a hint. > Thanks > Hermann > > df1 > Strand A1 A2 > rs3737728 u C T > rs6687776 u C T > rs9651273 u G A > > gr > GRanges with 3 ranges and 1 metadata column: > seqnames ranges strand | score > <rle> <iranges> <rle> | <character> > rs3737728 chr1 [1021415, 1021415] * | 0.340955 > rs6687776 chr1 [1030565, 1030565] * | 0.438123 > rs9651273 chr1 [1031540, 1031540] * | 0.196662 > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA > > > Perhaps just: mcols(gr) <- df1[names(gr),] > > > dput (df1) > structure(list(Strand = structure(c(1L, 1L, 1L), .Label = "u", class = > "factor"), > A1 = structure(c(2L, 2L, 3L), .Label = c("A", "C", "G", "T" > ), class = "factor"), A2 = structure(c(4L, 4L, 1L), .Label = c("A", > "C", "G", "T"), class = "factor")), .Names = c("Strand", > "A1", "A2"), class = "data.frame", row.names = c("rs3737728", > "rs6687776", "rs9651273")) > > dput (gr) > new("GRanges" > , seqnames = new("Rle" > , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", > "chr13", > "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", > "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", > "chr4_ctg9_hap1", > "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", > "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", > "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") > , lengths = 3L > , elementMetadata = NULL > , metadata = list() > ) > , ranges = new("IRanges" > , start = c(1021415L, 1030565L, 1031540L) > , width = c(1L, 1L, 1L) > , NAMES = c("rs3737728", "rs6687776", "rs9651273") > , elementType = "integer" > , elementMetadata = NULL > , metadata = list() > ) > , strand = new("Rle" > , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") > , lengths = 3L > , elementMetadata = NULL > , metadata = list() > ) > , elementMetadata = new("DataFrame" > , rownames = NULL > , nrows = 3L > , listData = structure(list(score = c("0.340955", "0.438123", > "0.196662")), .Names = "score") > , elementType = "ANY" > , elementMetadata = NULL > , metadata = list() > ) > , seqinfo = new("Seqinfo" > , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", > "chr15", > "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", > "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", > "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", > "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", > "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") > , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_) > , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, > NA, NA, > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, > NA, NA, NA) > , genome = c("hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19") > ) > , metadata = list(<s4 object="" of="" class="" structure("dataframe",="" package=""> "IRanges")>) > ) > > > > [[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 > [[alternative HTML version deleted]]