在特定列中保留具有值的行？

Question

我有一个像下面这样的 table 合并了多个数据，我想只保留在“-log10.qvalue”列中存在值的行。

输入：

chr_enhancer Start_enhancer End_enhancer                     source_enhancer.x                      source_marks.x -log10.qvalue.x                     source_enhancer.y -log10.qvalue.y                       source_enhancer -log10.qvalue
       chr1      100036100    100036650 Reilly_Hu_12Opcw_H3K4me2_rep1_2_merge                                .               .   Reilly_Hu_12Opcw_H3K4me2_rep1_2_merge               . Reilly_Hu_12Opcw_H3K4me2_rep1_2_merge             .
       chr1      100042226    100043575 Reilly_Hu_12Fpcw_H3K4me2_rep1_2_merge Fetalbrain.H3K4me1_narrow_peak_2501         2.145 Reilly_Hu_12Fpcw_H3K4me2_rep1_2_merge              .    Reilly_Hu_12Fpcw_H3K4me2_rep1_2_merge             1.254
       chr1      100042310    100043300            enhancer_atlas_Fetal_brain Fetalbrain.H3K4me1_narrow_peak_2501         5.145        enhancer_atlas_Fetal_brain               1.356            enhancer_atlas_Fetal_brain             6.325

输出：

 chr1      100042310    100043300            enhancer_atlas_Fetal_brain Fetalbrain.H3K4me1_narrow_peak_2501         5.145        enhancer_atlas_Fetal_brain               1.356            enhancer_atlas_Fetal_brain             6.325

Answer 1

首先使用 'grepl' 获取所有以 log10. 开头的列，然后使用 apply 检查每行中的 . 或 na 并求和。
最后，return 行，其中 sum(x=='.'| is.na(x))==0

df[apply(df[,grepl('log10.',names(df))],1,function(x)sum(x=='.'| is.na(x))==0),]


chr_enhancer Start_enhancer End_enhancer   source_enhancer.x     source_marks.x X.log10.qvalue.x
3         chr1      100042310    100043300 enhancer_atlas_Fetal_brain Fetalbrain.H3K4me1_narrow_peak_2501            5.145  
source_enhancer.y X.log10.qvalue.y            source_enhancer X.log10.qvalue
3 enhancer_atlas_Fetal_brain            1.356 enhancer_atlas_Fetal_brain          6.325

数据

 df <- read.table(text="chr_enhancer Start_enhancer End_enhancer                     source_enhancer.x                      source_marks.x -log10.qvalue.x                     source_enhancer.y -log10.qvalue.y                       source_enhancer -log10.qvalue
       chr1      100036100    100036650 Reilly_Hu_12Opcw_H3K4me2_rep1_2_merge                                .               .   Reilly_Hu_12Opcw_H3K4me2_rep1_2_merge               . Reilly_Hu_12Opcw_H3K4me2_rep1_2_merge             .
       chr1      100042226    100043575 Reilly_Hu_12Fpcw_H3K4me2_rep1_2_merge Fetalbrain.H3K4me1_narrow_peak_2501         2.145 Reilly_Hu_12Fpcw_H3K4me2_rep1_2_merge              .    Reilly_Hu_12Fpcw_H3K4me2_rep1_2_merge             1.254
       chr1      100042310    100043300            enhancer_atlas_Fetal_brain Fetalbrain.H3K4me1_narrow_peak_2501         5.145        enhancer_atlas_Fetal_brain               1.356            enhancer_atlas_Fetal_brain             6.325 
                 ",header=T)

在特定列中保留具有值的行？

Keep rows with valus in specific columns?

r

merge

split

bioconductor

数据