Returns a data.table
with a special print method that shows the top 2 most significant genes by contrast.
This data.table
contains columns:
doLRT=TRUE
)Some of these columns will contain NAs if they are not applicable for a particular component or contrast.
# S4 method for ZlmFit summary(object, logFC = TRUE, doLRT = FALSE, level = 0.95, ...)
ZlmFit
objectgetLogFC
.data.table
print.summaryZlmFit
#> #>zs <- summary(z)#>#>names(zs)#> [1] "datatable"print(zs)#> Fitted zlm with top 2 genes per contrast: #> ( log fold change Z-score ) #> primerid Stim.ConditionUnstim #> BCL2 -2.3* #> CCL3 -3.8*##Select `datatable` copmonent to get normal print method zs$datatable#> primerid component contrast ci.hi ci.lo coef #> 1: CCL2 D (Intercept) -2.44236757 -3.3620226 -2.9021951 #> 2: CCL3 D (Intercept) -1.58916186 -2.1962433 -1.8927026 #> 3: BCL2 D (Intercept) -1.56579681 -2.1670394 -1.8664181 #> 4: B3GAT1 D (Intercept) -2.69053309 -3.7525507 -3.2215419 #> 5: BAX D (Intercept) -0.33128091 -0.7564909 -0.5438859 #> 6: CCL2 S (Intercept) NA NA NA #> 7: CCL3 S (Intercept) NA NA NA #> 8: CCL2 C (Intercept) 22.37163738 19.2284654 20.8000514 #> 9: CCL3 C (Intercept) 23.15685816 20.9696836 22.0632709 #> 10: B3GAT1 S (Intercept) NA NA NA #> 11: BCL2 S (Intercept) NA NA NA #> 12: BAX S (Intercept) NA NA NA #> 13: B3GAT1 C (Intercept) 18.66804935 17.6920962 18.1800728 #> 14: BCL2 C (Intercept) 19.41604938 18.4701211 18.9430853 #> z #> 1: -12.3702861 #> 2: -12.2211896 #> 3: -12.1685068 #> 4: -11.8907750 #> 5: -5.0139783 #> 6: 9.5954215 #> 7: 19.3191106 #> 8: 25.9402614 #> 9: 39.5425379 #> 10: 43.2252343 #> 11: 46.9035705 #> 12: 60.4223239 #> 13: 73.0204876 #> 14: 78.5001723 #> [ reached getOption("max.print") -- omitted 22 rows ]