RNAseqDegs_limma: Helper Function For DEG Analysis of RNA-seq Data using limma...
In lusystemsbio/NetAct: NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity
RNAseqDegs_limma R Documentation
Helper Function For DEG Analysis of RNA-seq Data using limma + Voom
Description
Helper Function For DEG Analysis of RNA-seq Data using limma + Voom
Usage
RNAseqDegs_limma(counts, phenodata, complist, lfc, qval = 0.05)
Arguments
counts
Processed gene expression count data
phenodata
pData that provides batch & experimental conditions
complist
a vector of multiple comparisons in the format of contrasts in limma (e.g. c("A-B", "A-C", "B-C"))
lfc
(optional) log fold change constraints for DEGs
qval
q-value cutoff for DEG analysis (default: 0.05)
Value
DEresult: a list of DEG results, including those for each single comparison and those for the overall comparison.
Each DEG result is in the format of A list containing:
table: table of DEG results.
rank_vector: a vector of t-statistics for every gene.
degs: a vector of gene symbols for DEGs.
e: expression data (CPM).
e_batch: batch corrected expression.
lusystemsbio/NetAct documentation built on Sept. 7, 2024, 8:34 p.m.
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.
| RNAseqDegs_limma | R Documentation |
Helper Function For DEG Analysis of RNA-seq Data using limma + Voom
Description
Helper Function For DEG Analysis of RNA-seq Data using limma + Voom
Usage
RNAseqDegs_limma(counts, phenodata, complist, lfc, qval = 0.05)
Arguments
counts |
Processed gene expression count data |
phenodata |
pData that provides batch & experimental conditions |
complist |
a vector of multiple comparisons in the format of contrasts in limma (e.g. c("A-B", "A-C", "B-C")) |
lfc |
(optional) log fold change constraints for DEGs |
qval |
q-value cutoff for DEG analysis (default: 0.05) |
Value
DEresult: a list of DEG results, including those for each single comparison and those for the overall comparison. Each DEG result is in the format of A list containing: table: table of DEG results. rank_vector: a vector of t-statistics for every gene. degs: a vector of gene symbols for DEGs. e: expression data (CPM). e_batch: batch corrected expression.
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.