deseq2_pipe: Pipeline for DESeq2 analysis
In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R
Description
Usage
Arguments
Value
Description
Function to perform entire DESeq2 analysis, beginning with
a SummarizedExperiment and ending with list of differential genes and
generation of diagnostic plots along the way.
Usage
1
2
deseq2_pipe(se = NULL, block.column = NULL, adjust.method = "BH",
p.value = 0.05)
Arguments
se
SummarizedExperiment with an assay slot named counts_fil containing
the filtered counts and colData slot containing sample metadata.
block.column
The column in the samples metadata dataframe specifying
the block/additive effect column.
adjust.method
Method to be used for adjustment of nominal p-values.
May be one of "BH", "bonferroni", "holm", "hochberg", "hommel", "BY".
p.value
Value between 0 and 1. Adjusted p-value for the differential
expression analysis.
Value
List containing the DESeq2 DDS container, the raw results for each contrast
and the processed differential gene results.
anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.
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Description Usage Arguments Value
Description
Function to perform entire DESeq2 analysis, beginning with a SummarizedExperiment and ending with list of differential genes and generation of diagnostic plots along the way.
Usage
1 2 | deseq2_pipe(se = NULL, block.column = NULL, adjust.method = "BH",
p.value = 0.05)
|
Arguments
se |
SummarizedExperiment with an assay slot named counts_fil containing the filtered counts and colData slot containing sample metadata. |
block.column |
The column in the samples metadata dataframe specifying the block/additive effect column. |
adjust.method |
Method to be used for adjustment of nominal p-values. May be one of "BH", "bonferroni", "holm", "hochberg", "hommel", "BY". |
p.value |
Value between 0 and 1. Adjusted p-value for the differential expression analysis. |
Value
List containing the DESeq2 DDS container, the raw results for each contrast and the processed differential gene results.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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