Organizing the data for DESeq2

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

Bringing in data for DESeq2: sample order

Metadata meta_unordered

Raw counts counts_ordered

Bringing in data for DESeq2: sample order

rownames(wt_metadata)

 [1] "wt_normal3"  "smoc2_fibrosis2" "wt_fibrosis3"  "smoc2_fibrosis3" "smoc2_normal3"   "wt_normal1"     
 [7] "smoc2_normal4"  "wt_fibrosis2"  "wt_normal2"  "smoc2_normal1"  "smoc2_fibrosis1" "smoc2_fibrosis4"
[13] "wt_fibrosis4"  "wt_fibrosis1"

colnames(wt_rawcounts)

 [1] "wt_normal1"  "wt_normal2"  "wt_normal3"  "wt_fibrosis1"   "wt_fibrosis2"    "wt_fibrosis3"   
 [7] "wt_fibrosis4"  "smoc2_normal1"  "smoc2_normal3"  "smoc2_normal4"   "smoc2_fibrosis1" "smoc2_fibrosis2"
[13] "smoc2_fibrosis3" "smoc2_fibrosis4"

Bringing in data for DESeq2: sample order

all(rownames(wt_metadata) == colnames(wt_rawcounts))

FALSE

Matching order between vectors

Using the match() function:

match(vector1, vector2)

vector1: vector of values with the desired order

vector2: vector of values to reorder

output: the indices for how to rearrange vector2 to be in the same order as vector1

match(colnames(wt_rawcounts), rownames(wt_metadata)

6   9   1   14  8   3   13  10  5   7   11  2   4   12

Reordering using match() output:

idx <- match(colnames(wt_rawcounts), rownames(wt_metadata))

reordered_wt_metadata <- wt_metadata[idx, ]

View(reordered_wt_metadata)

Re-ordered metadata

all(rownames(reordered_wt_metadata) == colnames(wt_rawcounts))

TRUE

Re-ordered metadata

Ordered counts

Creating the DESeq2 object

# Create DESeq object
dds_wt <- DESeqDataSetFromMatrix(countData = wt_rawcounts,
                              colData = reordered_wt_metadata,
                              design = ~ condition)

deseq object

Let's practice!

RNA-Seq with Bioconductor in R