Adding columns to DEXSeqResults object
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Clyde • 0
@b19b1e82
Last seen 11 weeks ago
United States

I have a beginner question. How can I add a column to a DEXSeqResults object?

I ran DEXSeq on a transcriptome assembled with Trinity, so it has trinity_ids as gene symbols. However, these are not ideal to show on plots, so I ran blast and got some gene symbols. Now I want to add the column of gene symbols to the DEXSeqResults object before running plotDEXSeq but I am not sure how best to do so.

I have tried converting the object to a data frame, then adding the desired column, but I am not sure how to merge the data frame back to the DEXSeqResults object

# Load RData file
load("hali_transcriptome.dexseq.RData")

# Load blast results with gene symbols
col_names <- c("trinity_id", "gene_symbol")
blast_results <- read.delim("blastout_filtered.temp", header = FALSE, sep = "\t", row.names = NULL, col.names = col_names)

# Convert dxr1.sorted to a data frame
dxr1.sorted.df <- as.data.frame(dxr1.sorted)

# Merge dxr1.sorted with blast_results based on groupID
dxr1.sorted_with_genes <- merge(dxr1.sorted.df, blast_results, by.x = "groupID", by.y = "trinity_id", all.x = TRUE)

I would appreciate any help I can get with this issue.

DEXSeq • 231 views
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Alejandro Reyes ★ 1.9k
@alejandro-reyes-5124
Last seen 4 days ago
Novartis Institutes for BioMedical Reseā€¦

I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbols, which you could use to replace the gene ids in the dxr1 object

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