Detect differentially expressed Transcription Start Sites between two conditions (fit model)

Source: R/AllGenerics.R, R/detectDiffTSS.R

Detect differentially expressed Transcription Start Sites between two conditions (fit model)

fitDiffTSS(CSobject, TSSfile = NULL, groups, normalization = NULL,
  normFactors = NULL, outplots = NULL, plotRefSample, ncores = 1)

# S4 method for CapSet
fitDiffTSS(CSobject, TSSfile = NULL, groups,
  normalization = NULL, normFactors = NULL, outplots = NULL,
  plotRefSample, ncores = 1)

Arguments

CSobject	An object of class CapSet
TSSfile	A .bed file with TSS positions to test for differential TSS analysis. If left empty, the union of detected TSS present within the provided CSobject would be plotted.
groups	Character vector indicating the group into which each sample within the CSobject falls. the groups would be use to create a design matrix. As an example, replicates for one condition could be in the same group.
normalization	A character indicating the type of normalization to perform . Options are "windowTMM", "globalTMM" or NULL (don't compute normalization factors). If "windowTMM" is chosen, the normalization factors are calculated using the TMM method on 10 kb windows of the genome. "globalTMM" computes TMM normalization using counts from all the evaluated TSSs. If NULL, the external normalization factors can be used (provided using `normFactors`).
normFactors	external normalization factors (from Spike-Ins, for example).
outplots	Output pdf filename for plots. If provided, the plots for BCV, dispersion and MDS plot is created and saved in this file.
plotRefSample	Name of reference sample to plot for detection of composition bias in the data. Samples could be normalized using one of the provided normalization methods to control for composition bias.
ncores	No. of cores/threads to use

Value

An object of class DGEGLM-class.

Examples

# 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 diffTSS model
# NOT RUN {
# load a previously saved CapSet object
cs <- exampleCSobject()

# count reads on all TSS (union) and fit a model using replicates within groups
csfit <- fitDiffTSS(cs, groups = rep(c("wt","mut"), each = 2), normalization = "internal",
                     outplots = NULL, plotRefSample = "embryo1")
save(csfit, file = "diffTSS_fit.Rdata")
# }