[英]export file from R in bed format
I have a data.frame like this: 我有一个像这样的data.frame:
tab ->
elements scaffold start end Lengths
1 Dong-1_NVe_R4_Nematostella12_1 KQ415659.1 14193 14540 347
2 OK_SINE2/tRNA_Octopus44_1 KQ415659.1 68391 68626 235
3 RTE-8_NV_RTE_Nematostella6_1 KQ415659.1 69123 69884 761
4 Simple_repeat_(TCTT)n_1 KQ415659.1 70693 70827 134
5 RTE1-N1_LA_RTE_Loxodonta1_1 KQ415659.1 83088 83298 210
6 OK_SINE2/tRNA_Octopus93_5 KQ415659.1 91375 91569 194
7 Mariner1_BT_Mariner/Tc1_Bos3_3 KQ415659.1 101964 102378 414
8 Simple_repeat_(TA)nSimple_repeat96_1 KQ415659.1 104735 104877 142
9 AmnSINE2SINE/Deu30_2 KQ415659.1 110117 110255 138
10 Simple_repeat_(CATA)nSimple_repeat4_1 KQ415659.1 110622 111165 543
11 Simple_repeat_(TTA)nSimple_repeat9_1 KQ415659.1 112842 112959 117
12 TS2_SINE_Solanum4_1 KQ415659.1 117206 117467 261
13 RTE-8_NV_RTE_Nematostella6_3 KQ415659.1 118195 118433 238
and I would to export it into bed format from R. does anyone can help me? 并将其从R导出为床格式。有人可以帮助我吗?
Specifications like BED, GFF, and a few others attempt to standardize columns of your dataframe. 诸如BED,GFF之类的规范以及其他一些规范试图标准化数据框的列。 So, just get the columns of your dataframe in the correct order and then write your table.
因此,只需以正确的顺序获取数据框的列,然后编写表即可。
There's 3 required fields and then several more optional ones, as described by the folks at UCSC . 有3个必填字段,然后还有几个可选字段, 如UCSC的人员所述 。 Stick to the descriptions, write your data frame to a table, and you're good to go.
坚持说明,将数据框写到表中,一切就很好了。
bed <- tab[,c('scaffold', 'start', 'end', 'elements')]
colnames(bed) <- c('chrom', 'chromStart', 'chromEnd', 'name')
write.table(bed, "file.bed")
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