Generate a table from the DESeq2 results

Generate a tidy table with the results of DESeq2

deseqresult2df(res_de, FDR = NULL)

Arguments

res_de

A DESeqResults object.

FDR

Numeric value, specifying the significance level for thresholding adjusted p-values. Defaults to NULL, which would return the full set of results without performing any subsetting based on FDR.

Value

A tidy data.frame with the results from differential expression, sorted by adjusted p-value. If FDR is specified, the table contains only genes with adjusted p-value smaller than the value.

Examples

data(res_de_macrophage, package = "GeneTonic")
head(res_macrophage_IFNg_vs_naive)
#> log2 fold change (MLE): condition IFNg vs naive 
#> Wald test p-value: condition IFNg vs naive 
#> DataFrame with 6 rows and 7 columns
#>                  baseMean log2FoldChange     lfcSE      stat      pvalue
#>                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
#> ENSG00000000003   171.571     -0.2822450 0.3005710   0.00000 1.00000e+00
#> ENSG00000000419   967.751      0.0391223 0.0859708   0.00000 1.00000e+00
#> ENSG00000000457   682.433      1.2846179 0.1969067   1.44545 1.48333e-01
#> ENSG00000000460   262.963     -1.4718762 0.2186916  -2.15772 3.09493e-02
#> ENSG00000000938  2660.102      0.6754781 0.2360530   0.00000 1.00000e+00
#> ENSG00000000971  3052.123      4.9871107 0.4964284   8.03159 9.62155e-16
#>                        padj      SYMBOL
#>                   <numeric> <character>
#> ENSG00000000003 1.00000e+00      TSPAN6
#> ENSG00000000419 1.00000e+00        DPM1
#> ENSG00000000457 1.00000e+00       SCYL3
#> ENSG00000000460 4.09728e-01    C1orf112
#> ENSG00000000938 1.00000e+00         FGR
#> ENSG00000000971 1.37057e-13         CFH
res_df <- mosdef::deresult_to_df(res_macrophage_IFNg_vs_naive)
head(res_df)
#>                              id   baseMean log2FoldChange     lfcSE     stat
#> ENSG00000125347 ENSG00000125347 30585.0749       5.560124 0.2182663 20.89248
#> ENSG00000162645 ENSG00000162645 36790.5921       6.665804 0.2865732 19.77088
#> ENSG00000111181 ENSG00000111181   688.5779       4.710592 0.1961023 18.92172
#> ENSG00000174944 ENSG00000174944  1324.3975       9.863904 0.4715127 18.79886
#> ENSG00000100336 ENSG00000100336  2551.4789       8.708551 0.4214096 18.29230
#> ENSG00000145365 ENSG00000145365  3637.2221       5.193448 0.2368542 17.70476
#>                       pvalue         padj  SYMBOL
#> ENSG00000125347 6.268470e-97 1.116164e-92    IRF1
#> ENSG00000162645 5.304222e-87 4.722349e-83    GBP2
#> ENSG00000111181 7.555181e-80 4.484252e-76 SLC6A12
#> ENSG00000174944 7.715124e-79 3.434388e-75  P2RY14
#> ENSG00000100336 9.530829e-75 3.394119e-71   APOL4
#> ENSG00000145365 3.853076e-70 1.143465e-66    TIFA