由于类不同，我们可以在转换为data.frame后使用rownames_to_column

class(resSig)
[1] "DESeqResults"
attr(,"package")
[1] "DESeq2"

我们使用as.data.frame转换为 Dataframe ，然后执行rownames_to_column

library(dplyr)
library(tibble)
resSig <- resSig %>%
   as.data.frame %>%
   rownames_to_column("transcript_ID")

• 输出

resSig 
       transcript_ID   baseMean log2FoldChange     lfcSE     stat       pvalue         padj
1 ENSMUST00000103410.3 15237.9255       1.667017 0.4726054 3.527291 4.198356e-04 0.0097788597
2 ENSMUST00000194738.6   134.4450       1.909577 0.3913188 4.879849 1.061670e-06 0.0001551706
3 ENSMUST00000178282.3 24953.2773       1.523272 0.3601117 4.229998 2.336935e-05 0.0013347592
4 ENSMUST00000200568.2   675.4079       2.284544 0.5577937 4.095680 4.209318e-05 0.0020138101
5 ENSMUST00000196768.2    69.8793       2.997955 0.8722588 3.437002 5.881911e-04 0.0122055138
6 ENSMUST00000197515.2   119.6366       3.170698 0.7820734 4.054220 5.030189e-05 0.0022939429
> str(resSig)
data.frame':    6 obs. of  7 variables:
 $ transcript_ID : chr  "ENSMUST00000103410.3" "ENSMUST00000194738.6" "ENSMUST00000178282.3" "ENSMUST00000200568.2" ...
 $ baseMean      : num  15237.9 134.4 24953.3 675.4 69.9 ...
 $ log2FoldChange: num  1.67 1.91 1.52 2.28 3 ...
 $ lfcSE         : num  0.473 0.391 0.36 0.558 0.872 ...
 $ stat          : num  3.53 4.88 4.23 4.1 3.44 ...
 $ pvalue        : num  4.20e-04 1.06e-06 2.34e-05 4.21e-05 5.88e-04 ...
 $ padj          : num  0.009779 0.000155 0.001335 0.002014 0.012206 ...

注意：OP的最后一段代码在转换为data.frame后也可以工作

resSig <- as.data.frame(resSig)
resSig <- cbind(transcript_ID=rownames(resSig), resSig)
row.names(resSig) <- NULL
> resSig
         transcript_ID   baseMean log2FoldChange     lfcSE     stat       pvalue         padj
1 ENSMUST00000103410.3 15237.9255       1.667017 0.4726054 3.527291 4.198356e-04 0.0097788597
2 ENSMUST00000194738.6   134.4450       1.909577 0.3913188 4.879849 1.061670e-06 0.0001551706
3 ENSMUST00000178282.3 24953.2773       1.523272 0.3601117 4.229998 2.336935e-05 0.0013347592
4 ENSMUST00000200568.2   675.4079       2.284544 0.5577937 4.095680 4.209318e-05 0.0020138101
5 ENSMUST00000196768.2    69.8793       2.997955 0.8722588 3.437002 5.881911e-04 0.0122055138
6 ENSMUST00000197515.2   119.6366       3.170698 0.7820734 4.054220 5.030189e-05 0.0022939429

写入该文件可获得

write.table(resSig, file = file.path(getwd(), "Downloads", 
    "ivan.txt"), row.names = FALSE, quote = FALSE)

• 输出