在R中使用tidyr包，使用道集()“无效列规范”

Question

我还在学习如何使用tidyr。我想使用“gene_ID()”将列分成多个行，并通过在适用的情况下复制“”列来保留它。示例输入数据：

    gene_ID path1   path2   path3   path4   path5   path6   path7   path8
CAMNT_0043146643    RNA transport                           
CAMNT_0029561721    Ribosome                            
CAMNT_0024703307    Sphingolipid signaling pathway  Lysosome                        
CAMNT_0020981363    mRNA surveillance pathway   Hippo signaling pathway cAMP signaling pathway  cGMP - PKG signaling pathway    Regulation of actin cytoskeleton    Meiosis - yeast Oocyte meiosis  Focal adhesion
CAMNT_0020021387    Spliceosome Protein processing in endoplasmic reticulum MAPK signaling pathway  Endocytosis             
CAMNT_0003293445    Spliceosome Protein processing in endoplasmic reticulum MAPK signaling pathway  Endocytosis             

所需输出数据示例：

gene_ID Pathway
CAMNT_0043146643    RNA transport
CAMNT_0029561721    Ribosome
CAMNT_0024703307    Lysosome
CAMNT_0024703307    Sphingolipid signaling pathway
CAMNT_0020981363    mRNA surveillance pathway
CAMNT_0020981363    Hippo signaling pathway
CAMNT_0020981363    cAMP signaling pathway
CAMNT_0020981363    cGMP - PKG signaling pathway
CAMNT_0020981363    Regulation of actin cytoskeleton
CAMNT_0020981363    Meiosis - yeast
CAMNT_0020981363    Oocyte meiosis
CAMNT_0020981363    Focal adhesion
CAMNT_0020021387    Spliceosome
CAMNT_0020021387    Protein processing in endoplasmic reticulum
CAMNT_0020021387    MAPK signaling pathway
CAMNT_0020021387    Endocytosis
CAMNT_0003293445    Spliceosome
CAMNT_0003293445    Protein processing in endoplasmic reticulum
CAMNT_0003293445    MAPK signaling pathway
CAMNT_0003293445    Endocytosis

目前，我正在尝试：

temp<-gather(extract,"gene_ID",path1:path8)

但是我得到了一条错误消息：" error :无效的列规范“--我尝试过在输入df时使用和不带标头的方法，但是同样的错误也会发生。我愿意使用另一种方法，但我对"NAs“有问题，因为并非所有行"gene_IDs”都有相同的列数。

关于如何进行的建议？

Answer 1

df <- data.frame(x = c("a", "b", "c","d","e"),
                 path1=c("test1","test1","test2","test2","test3"),
                 path2=c("testa","","testg","testd",""))
library(reshape2)
df[df==""] <- NA
melt(df, id.vars="x", na.rm=T)
#   x variable value
# 1 a    path1 test1
# 2 b    path1 test1
# 3 c    path1 test2
# 4 d    path1 test2
# 5 e    path1 test3
# 6 a    path2 testa
# 8 c    path2 testg
# 9 d    path2 testd

Answer 2

下面是一个tidyr解决方案：

df %>%
  gather(path, Pathway, path1, path2) %>%
  filter(Pathway != "") %>%
  select(-path)

  x Pathway
1 a   test1
2 b   test1
3 c   test2
4 d   test2
5 e   test3
6 a   testa
7 c   testg
8 d   testd