Analysis of gene differential expression.

Analyzes gene-level differential expression using DESeq2 method (Love et al., 2014).

deGene(object,comparePairs=list(c("control","treat")), pval = 0.01,
 useMultiCore=FALSE, numCores = NULL)

# S4 method for TSSr
deGene(
  object,
  comparePairs = list(c("control", "treat")),
  pval = 0.01,
  useMultiCore = FALSE,
  numCores = NULL
)

Arguments

object	A TSSr object.
comparePairs	Specified list of sample pairs for comparison with DESeq2 method.
pval	Genes with adjusted p value >= pVal will be returned. Default value = 0.01.
useMultiCore	Logical indicating whether multiple cores are used (TRUE) or not (FALSE). Default is FALSE.
numCores	Number of cores are used in clustering step. Used only if useMultiCore = TRUE. Default is NULL.

Examples

# \donttest{
deGene(exampleTSSr,comparePairs=list(c("control","treat")), pval = 0.01)
#> 
#> Calculating gene differential expression...
#> converting counts to integer mode
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
# }