在嵌套列表中使用R和复杂数据帧进行子设置

I have a very large and complex data frame from a ChIP-seq experiment. This data frame contains binding positions and scores for small DNA sequencing reads. The output is from the program spp. The data is organized by chromosome with names(spp_output$npl) giving a list of all of the chromosomes. If I pick a chromosome (let say chr1) the output of I have a very large and complex data frame from