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Learn the steps to convert DGEList data format into MicrobiomeStat data format. |
This guide will assist you in converting DGEList data format into MicrobiomeStat format.
Before we proceed with the conversion, let's examine the original structure of our DGEList data:
Original structure of the DGEList data.
Now, follow the steps below to convert the DGEList data:
# Load necessary packages
library(airway)
library(DESeq2)
library(edgeR)
# Load dataset
data("airway")
dds <- DESeqDataSet(airway, design = ~ cell + dex)
dge <- DGEList(counts = counts(dds), group = dds$dex)
# Convert DGEList to MicrobiomeStat data object
data.obj <- mStat_convert_DGEList_to_data_obj(dge)After conversion, let's take a look at the transformed data structure:
Structure of the MicrobiomeStat data object after importing DGEList data.
By using the mStat_convert_DGEList_to_data_obj function, you can effectively convert:
- dge.obj: Your existing DGEList object.
The resultant MicrobiomeStat data object includes:
- feature.tab: A matrix populated with counts data.
- meta.dat: A data frame detailing the sample information.
As part of the conversion process, features with a sum of zero from the counts data are filtered out to maintain data relevance.