... Ok. If you set ignore.strand = TRUE, you will get the one with shortest distance.
distanceToNearest(x, TSS, ignore.strand= TRUE)
Hits object with 1 hit and 1 metadata column:
queryHits subjectHits | distance
<integer> <integer> | <integer>
 1 ...
... Looks like that you are trying to annotate peaks. If that is the case, you might want to try the function annotatePeakInBatch in the ChIPpeakAnno package http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html.
Activity on a post you are following on support.bioco ...
The most recent version of ATACseqQC at http://bioconductor.org/packages/devel/bioc/html/ATACseqQC.html should run faster.
... Hi, could you please try with upstream.cutoff = 0, downstream.cutoff = 0? Also could you please provide your R session information by typing sessionInfo()? Thanks!
GUIDEseq package can be used to analyze CIRCLE-seq too. During the preprocessing steps, you will not need to remove adaptors introduced in the GUIDE-seq protocol. In addition, you will need to set the max.R1.len =150 and max.R2.len = 150 using the GUIDEseqAnalysis function in GUIDEseq packag ...
Here is a description of the parameter useEfficacyFromInputSeq.
Default FALSE. If set to TRUE, summary file will contain gRNA efficacy calculated from input sequences instead of from off-target analysis. Set it to TRUE if the input sequence is from a different species than the one used for o ...