Load GSEA software results into R
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6 weeks ago
ryme ▴ 10

Does anyone know how to import/read/load the results of the gene set enrichment analysis generated from the GSEA software into R? I want to visualize the results, plot them and create heatmaps in R using ggplot, clusterprofiler, etc.

Thanks!

GSEA R plot • 297 views
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What have you tried?

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I am new to bioinformatics and R. I haven't tried anything yet. I want to import the data/results generated from GSEA software into R but I don't know how to do it.

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In that case, have you Googled "load data into R"? Have you looked at the data you wish to load and characterized it in terms that data processing software (anything from Excel to python to R to Tableau) can understand?

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I suggest to start with R-studio. There, you can use a data import wizard that is very similar to the Excel data importer. It should be able to import about anything in text format. Click Environment (right upper section of screen) -> Import Dataset -> From text (base or readr) and try it out, the code that is generated is "almost self-explaining".

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6 weeks ago
YanO ▴ 140

Your results from the GSEA software will be stored in two files called gsea_report_for_na_pos_12345.tsv and gsea_report_for_na_neg_12345.tsv in whatever folder you selected as your output folder when using the software. To load into R you can use:

pos_result <- read.delim("path_to_folder_with_results/gsea_report_for_na_pos_12345.tsv")

(You also mention you want to use clusterprofiler to visualise the results - I tried to replot results of the Broad's GSEA software with clusterprofiler with no luck, it might not be possible, see this post: be great if someone could prove me wrong here.)

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Hi, as @YanO said you must load the .tsv files generated after analysis using read.delim command. In this case, if you want to plot your data (dotplots, barplots or a heatmap) a good option is to use ggplot2 and look for the better plotting options.

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I've moved this to a comment as the post merely says "Use ggplot2 for plotting" - it does not answer the top level question in a way that is not already addressed by YanO's answer.

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