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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covplot #208

Open fork16 opened 1 year ago

fork16 commented 1 year ago

y叔您好,非常感谢能提供covplot这个函数出来,但是我这里想自己给条形图的颜色添加透明度,我把covplot.r脚本复制下来并library相应的包逐行运行,在getChrCov函数内的 cov <- lapply(peak.cov, slice, lower=1) 命令出现以下错误

library(ChIPseeker)
library(ggplot2)
library(GenomeInfoDb)
library(S4Vectors)
library(dplyr)
library(magrittr)
files <- getSampleFiles()
peak=GenomicRanges::GRangesList(CBX6=readPeakFile(files[[4]]),CBX7=readPeakFile(files[[5]]))
peak.gr <- peak$CBX6
weight <- mcols(peak.gr)[['V5']]
peak.cov <- coverage(peak.gr, weight=weight)
cov <- lapply(peak.cov, slice, lower=1)
Error in UseMethod("slice") : 
  no applicable method for 'slice' applied to an object of class "c('Rle', 'Vector', 'Annotated', 'vector_OR_Vector')"

我在网上搜索这类型的问题,说是slice所用的包dplyt版本太低,但是我认为不应该是版本问题,因为直接运行ChIpseeker::covplot 是没有报错的。请问我应该如何做才能成功运行修改后的covplot函数? 我的ChIpseeker版本是1.35.0