getFeatureCountsBig {hiAnnotator} | R Documentation |
Given a query object and window size(s), the function finds all the rows in
subject which are <= window size/2 distance away. Note that here counting is
done using midpoint of the ranges in query instead of start-stop boundaries.
The counts will differ slightly when compared to
getFeatureCounts
.
getFeatureCountsBig( sites.rd, features.rd, colnam = NULL, widths = c(1000, 10000, 1e+06) )
sites.rd |
GRanges object to be used as the query. |
features.rd |
GRanges object to be used as the subject or the annotation table. |
colnam |
column name to be added to sites.rd for the newly calculated annotation...serves as a prefix to windows sizes! |
widths |
a named/numeric vector of window sizes to be used for casting
a net around each position. Default: |
a GRanges object with new annotation columns appended at the end of sites.rd. There will be a column for each width defined in widths parameter. If widths was a named vector i.e. c("100bp"=100,"1K"=1000), then the colname parameter will be pasted together with width name else default name will be generated by the function.
makeGRanges
, getNearestFeature
,
getSitesInFeature
, getFeatureCounts
.
# Convert a dataframe to GRanges object data(sites) alldata.rd <- makeGRanges(sites, soloStart = TRUE) data(genes) genes.rd <- makeGRanges(genes) geneCounts1 <- getFeatureCounts(alldata.rd, genes.rd, "NumOfGene") ## Not run: geneCounts2 <- getFeatureCountsBig(alldata.rd, genes.rd, "NumOfGene") identical(geneCounts1, geneCounts2) ## End(Not run)