Hi, I am a totally new to R-studio and it's software. I have been trying to follow the tutorial posted on "https://stephenturner.github.io/deseq-to-fgsea/#load_some_results_from_deseq2"
I had used the using FGSEA package on, "https://bioconductor.org/packages/release/bioc/html/fgsea.html" and had followed the Installation for R.
1: Is there a more detail and step by step tutorial for this. I had found some but they required some knowledge of coding? 2: How do I import my own data into the software so the GSEA is shown as in website 1. 3: Here is an example of my data for GSEA:
#1.2
545 6
NAME description WTcontrol1 WTcontrol2 WTcontrol3 WTDTnormalized1 WTDTnormalized2 WTDTnormalized3
ENSMUSG00000071103 1700029J07Rik -0.2826271 0.03396225 -0.008006096 0.3456192 0.43789434 0.49301577
ENSMUSG00000100573 1700081H04Rik -0.002503395 -0.01300478 0.002502918 -0.084319115 -0.0729208 -0.05217266
ENSMUSG00000097162 2310010J17Rik -0.031499863 -0.18440628 -0.04216671 0.16484451 0.18860006 0.13092566
ENSMUSG00000032062 2310030G06Rik -0.23690319 -0.21158266 -0.102458 0.16413021 0.24428272 0.31841516
ENSMUSG00000072852 2310040G07Rik -0.03087902 -0.15501404 -0.079369545 0.268198 0.17418766 0.1296587
I am currently stuck on
library(airway) ddsSE <- DESeqDataSet(airway, design = ~ cell + dex) ddsSE <- DESeq(ddsSE) res <- results(ddsSE, tidy = TRUE) readr::write_csv(res, path="data/deseq-results-tidy-human-airway.csv")
What are the options to replace "airway" with so I can run my own sample opposed to
library(tidyverse) res <- read_csv("data/deseq-results-tidy-human-airway.csv") res
The option is to point to your own data rather than using demo data. Have you read the
DESeq2
vignette I pointed to?Thanks for the assist. Do you know how to decrease the font of the pathway so it is more legible?
If you are talking about the
ggplot
part, then yes. See?theme
, in particular theaxis.text.y
argument, as well as?element_text
.