detectDiffTSS {icetea} | R Documentation |
Detect differentially expressed Transcription Start Sites between two conditions (test)
detectDiffTSS(fit, testGroup, contGroup, TSSfile = NULL, MAplot_fdr = NA) ## S4 method for signature 'DGEGLM' detectDiffTSS(fit, testGroup, contGroup, TSSfile = NULL, MAplot_fdr = NA) ## S4 method for signature 'DESeqDataSet' detectDiffTSS(fit, testGroup, contGroup, MAplot_fdr = NA)
fit |
DGEGLM object (output of |
testGroup |
Test group name |
contGroup |
Control group name |
TSSfile |
The TSS .bed file used for |
MAplot_fdr |
FDR threshold to mark differentially expressed TSS in MAplot (NA = Don't make an MAplot) |
A GRanges
object containing p-values of differential expression for each TSS.
# before running this # 1. Create a CapSet object # 2. de-multiplex the fastqs # 3. map them # 4. filter duplicate reads from mapped BAM # 5. detect TSS # 6. fit the diff TSS model. ## Not run: # load a previously saved DGEGLM object from step 5 csfit <- load("diffTSS_fit.Rdata") dir <- system.file("extdata", package = "icetea") # detect differentially expressed TSS between groups (return MA plot) detectDiffTSS(csfit, testGroup = "mut", controlGroup = "wt", tssFile = file.path(dir, "testTSS_merged.bed"), MAplot_fdr = 0.05) ## End(Not run) ## Not run: # load a previously saved DGEGLM object from step 5 csfit <- load("diffTSS_fit.Rdata") dir <- system.file("extdata", package = "icetea") # detect differentially expressed TSS between groups (return MA plot) detectDiffTSS(csfit, testGroup = "mut", controlGroup = "wt", MAplot_fdr = 0.05) ## End(Not run)