You can use ChIPseeker.
The only input for annotation is the bed file and TxDb object which can be generated by gtf file downloaded from UCSC.
If you are using human hg19, you can use the following TxDb available in Bioconductor:
https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts.html.
Read the documents of ChIPseeker, especially the vignette to find out more.
DEMO
just demonstrate the usage. The bed file here is not related to lincRNA.
> require(ChIPseeker)
> getSampleFiles() -> x
> x[[1]]
[1] "/Library/R/library/ChIPseeker/extdata/GEO_sample_data/GSM1174480_ARmo_0M_peaks.bed.gz"
> peak=readPeakFile(x[[1]])
> peak
GRanges object with 812 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrX [ 61728297, 61728780] *
[2] chr10 [ 39105185, 39105362] *
[3] chrY [ 13137266, 13137499] *
[4] chr11 [114049918, 114050234] *
[5] chrY [ 13107715, 13107867] *
... ... ... ...
[808] chrX [ 49239222, 49239305] *
[809] chrX [ 54945698, 54945789] *
[810] chrX [ 61817143, 61817176] *
[811] chrX [147048421, 147048507] *
[812] chrY [ 887860, 887931] *
-------
seqinfo: 24 sequences from an unspecified genome; no seqlengths
> require("TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts")
> txdb=TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts
> xx=annotatePeak(peak, TxDb=txdb)
>> preparing features information... 2016-10-06 14:31:03
>> identifying nearest features... 2016-10-06 14:31:03
>> calculating distance from peak to TSS... 2016-10-06 14:31:04
>> assigning genomic annotation... 2016-10-06 14:31:04
>> assigning chromosome lengths 2016-10-06 14:31:06
>> done... 2016-10-06 14:31:06
> xx
Annotated peaks generated by ChIPseeker
812/812 peaks were annotated
Genomic Annotation Summary:
Feature Frequency
6 Promoter (<=1kb) 0.7389163
7 Promoter (1-2kb) 1.2315271
8 Promoter (2-3kb) 0.3694581
4 Other Exon 0.6157635
1 1st Intron 3.2019704
5 Other Intron 3.0788177
3 Downstream (<=3kb) 0.4926108
2 Distal Intergenic 90.2709360
> as.GRanges(xx)
GRanges object with 812 ranges and 9 metadata columns:
seqnames ranges strand | annotation geneChr
<Rle> <IRanges> <Rle> | <character> <integer>
[1] chrX [ 61728297, 61728780] * | Distal Intergenic 23
[2] chr10 [ 39105185, 39105362] * | Distal Intergenic 10
[3] chrY [ 13137266, 13137499] * | Distal Intergenic 24
[4] chr11 [114049918, 114050234] * | Distal Intergenic 11
[5] chrY [ 13107715, 13107867] * | Distal Intergenic 24
geneStart geneEnd geneLength geneStrand geneId
<integer> <integer> <integer> <integer> <character>
[1] 61998718 61999787 1070 1 TCONS_l2_00030232
[2] 38933913 38982200 48288 2 TCONS_l2_00004140
[3] 13362085 13370619 8535 2 TCONS_l2_00030933
[4] 113887644 113888813 1170 2 TCONS_00019764
[5] 13362085 13370619 8535 2 TCONS_l2_00030933
transcriptId distanceToTSS
<character> <numeric>
[1] TCONS_l2_00030232 -269938
[2] TCONS_l2_00004140 -122985
[3] TCONS_l2_00030933 233120
[4] TCONS_00019764 -161105
[5] TCONS_l2_00030933 262752
-------
seqinfo: 24 sequences from hg19 genome
>
