Returns a data.table
with a special print method that shows the top 2 most significant genes by contrast.
This data.table
contains columns:
the gene
C=continuous, D=discrete, logFC=log fold change, S=combined using Stouffer's method, H=combined using hurdle method
the coefficient/contrast of interest
upper bound of confidence interval
lower bound of confidence interval
point estimate
z score (coefficient divided by standard error of coefficient)
likelihood ratio test p-value (only if 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, ...)
object | A |
---|---|
logFC | If TRUE, calculate log-fold changes, or output from a call to |
doLRT | if TRUE, calculate lrTests on each coefficient, or a character vector of such coefficients to consider. |
level | what level of confidence coefficient to return. Defaults to 95 percent. |
... | ignored |
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 #> 15: BAX C (Intercept) 19.31259333 18.4934991 18.9030462 #> 16: CCL3 logFC Stim.ConditionUnstim -1.03709089 -3.2491890 -2.1431399 #> 17: CCL3 D Stim.ConditionUnstim -0.28878236 -2.5303707 -1.4095765 #> 18: BAX C Stim.ConditionUnstim -0.21303964 -1.9052758 -1.0591577 #> 19: BCL2 logFC Stim.ConditionUnstim -0.17786584 -2.4494721 -1.3136690 #> 20: CCL3 S Stim.ConditionUnstim NA NA NA #> 21: BCL2 S Stim.ConditionUnstim NA NA NA #> 22: BCL2 D Stim.ConditionUnstim 0.09775406 -1.6221758 -0.7622108 #> 23: BCL2 C Stim.ConditionUnstim 0.66939860 -2.1945414 -0.7625714 #> 24: B3GAT1 C Stim.ConditionUnstim 0.57039007 -1.7528431 -0.5912265 #> 25: B3GAT1 S Stim.ConditionUnstim NA NA NA #> 26: CCL2 C Stim.ConditionUnstim 2.22026031 -5.3168014 -1.5482705 #> 27: CCL2 S Stim.ConditionUnstim NA NA NA #> 28: BAX S Stim.ConditionUnstim NA NA NA #> 29: CCL2 logFC Stim.ConditionUnstim 0.70894380 -1.1676533 -0.2293547 #> 30: CCL3 C Stim.ConditionUnstim 3.45685041 -5.5611013 -1.0521254 #> 31: CCL2 D Stim.ConditionUnstim 0.90444296 -1.2421537 -0.1688554 #> 32: B3GAT1 logFC Stim.ConditionUnstim 0.60696199 -0.8305510 -0.1117945 #> 33: B3GAT1 D Stim.ConditionUnstim 1.07670176 -1.3704909 -0.1468946 #> 34: BAX logFC Stim.ConditionUnstim 3.15942619 -0.9870469 1.0861896 #> 35: BAX D Stim.ConditionUnstim 0.80556556 -0.1194848 0.3430404 #> primerid component contrast ci.hi ci.lo coef #> 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 #> 15: 90.4640483 #> 16: -3.7977313 #> 17: -2.4649658 #> 18: -2.4534531 #> 19: -2.2668927 #> 20: -2.0663811 #> 21: -1.9664048 #> 22: -1.7371707 #> 23: -1.0437456 #> 24: -0.9975604 #> 25: -0.8717615 #> 26: -0.8052354 #> 27: -0.7874231 #> 28: -0.7069721 #> 29: -0.4790874 #> 30: -0.4573384 #> 31: -0.3083490 #> 32: -0.3048504 #> 33: -0.2352966 #> 34: 1.0268450 #> 35: 1.4536435 #> z