Description Usage Arguments Value Author(s)
View source: R/run.DESeq2_Salmon.r View source: R/run.DESeq2_Salmon.r View source: R/run.DESeq2_trans.r
Wrapper to run DESeq2: create the DESeqDataSet
, normalize data, estimate dispersions, statistical testing...
Wrapper to run DESeq2: create the DESeqDataSet
, normalize data, estimate dispersions, statistical testing...
Wrapper to run DESeq2: create the DESeqDataSet
, normalize data, estimate dispersions, statistical testing...
1 2 3 4 5 6 7 8 9 10 11  run.DESeq2_trans(counts, target, varInt, batch = NULL,
locfunc = "median", fitType = "parametric", pAdjustMethod = "BH",
alpha = 0.05, ...)
run.DESeq2_trans(counts, target, varInt, batch = NULL,
locfunc = "median", fitType = "parametric", pAdjustMethod = "BH",
alpha = 0.05, ...)
run.DESeq2_trans(counts, target, varInt, batch = NULL,
locfunc = "median", fitType = "parametric", pAdjustMethod = "BH",
alpha = 0.05, ...)

counts 

target 
target 
varInt 
name of the factor of interest (biological condition) 
batch 
batch effect to take into account ( 
locfunc 

fitType 
meanvariance relationship: "parametric" (default) or "local" 
pAdjustMethod 
pvalue adjustment method: 
alpha 
significance threshold to apply to the adjusted pvalues 
... 
optional arguments to be passed to 
independentFiltering 

counts 

target 
target 
varInt 
name of the factor of interest (biological condition) 
batch 
batch effect to take into account ( 
locfunc 

fitType 
meanvariance relationship: "parametric" (default) or "local" 
pAdjustMethod 
pvalue adjustment method: 
independentFiltering 

alpha 
significance threshold to apply to the adjusted pvalues 
... 
optional arguments to be passed to 
counts 

target 
target 
varInt 
name of the factor of interest (biological condition) 
batch 
batch effect to take into account ( 
locfunc 

fitType 
meanvariance relationship: "parametric" (default) or "local" 
pAdjustMethod 
pvalue adjustment method: 
independentFiltering 

alpha 
significance threshold to apply to the adjusted pvalues 
... 
optional arguments to be passed to 
A list containing the dds
object (DESeqDataSet
class), the results
objects (DESeqResults
class) and the vector of size factors
A list containing the dds
object (DESeqDataSet
class), the results
objects (DESeqResults
class) and the vector of size factors
A list containing the dds
object (DESeqDataSet
class), the results
objects (DESeqResults
class) and the vector of size factors
Aditya Narayan Sarangi
Aditya Narayan Sarangi
Aditya Narayan Sarangi
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