YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
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bug fix #191 #194

Closed MingLi-929 closed 2 years ago

MingLi-929 commented 2 years ago

The reported bugs exist #191.

files <- getSampleFiles()
peak <- readPeakFile(files[[4]])
test.range <- GRanges(seqnames = c('chr1','chrX','chr1'),ranges = IRanges(c(815094,139583955,3816546), 
                                                                          width=200,gene_id=c('1','100','1000')))
attr(test.range,'type') <- 'body'
attr(test.range,'label') <- c('TSS','TTS')
attr(test.range,'upstream') <- NULL
attr(test.range,'downstream') <- NULL

test.matrix <- getTagMatrix(peak,windows = test.range,nbin = 20,weightCol = 'V5')
test.matrix

The pr fixes them.

> test.matrix
       [,1]   [,2]   [,3]   [,4]   [,5]   [,6]   [,7]   [,8]   [,9]  [,10]  [,11]
[1,] 295.76 295.76 295.76 295.76 295.76 295.76 295.76 295.76 295.76 295.76 295.76
[2,]  57.57  57.57  57.57  57.57  57.57  57.57  57.57  57.57  57.57  57.57  57.57
[3,] 918.73 918.73 918.73 918.73 918.73 918.73 918.73 918.73 918.73 918.73 918.73
      [,12]  [,13]  [,14]  [,15]  [,16]  [,17]  [,18]  [,19]  [,20]
[1,] 295.76 295.76 295.76 295.76 295.76 295.76 295.76 295.76 295.76
[2,]  57.57  57.57  57.57  57.57  57.57  57.57  57.57  57.57  57.57
[3,] 918.73 918.73 918.73 918.73 918.73 918.73 918.73 918.73 918.73
attr(,"type")
[1] "body"
attr(,"label")
[1] "TSS" "TTS"
attr(,"is.binning")
[1] TRUE