changes to module 3, part 4

griffithlab · Jun 13, 2024 · 05a7828 · 05a7828
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Showing 3 changed files with 15 additions and 9 deletions.
diff --git a/_posts/0003-04-03-DE_Visualization_AdvancedR.md b/_posts/0003-04-03-DE_Visualization_AdvancedR.md
@@ -49,23 +49,24 @@ library(ggrepel)
 #Set working directory where results files exist
 datadir = "~/workspace/rnaseq/de/ballgown/ref_only"
 # datadir = "/cloud/project/data/bulk_rna"
-# outdir = "/cloud/project/outdir"
+outdir = "~/workspace/rnaseq/de/manual_viz"
+if (!dir.exists(outdir)) dir.create(outdir)
 
 setwd(datadir)
 
 # List the current contents of this directory
 dir()
 
 #Import expression results (TPM values) from the HISAT2/Stringtie pipeline (http://genomedata.org/rnaseq-tutorial/results/cshl2022/rnaseq/gene_tpm_all_samples.tsv)
-gene_expression=read.table("gene_tpm_all_samples.tsv", header=TRUE, stringsAsFactors=FALSE, row.names=1)
+gene_expression=read.table("~/workspace/rnaseq/expression/stringtie/ref_only/gene_tpm_all_samples.tsv", header=TRUE, stringsAsFactors=FALSE, row.names=1)
 
 #Import gene name mapping file (http://genomedata.org/rnaseq-tutorial/results/cshl2022/rnaseq/ENSG_ID2Name.txt)
-gene_names=read.table("ENSG_ID2Name.txt", header=TRUE, stringsAsFactors=FALSE)
+gene_names=read.table("~/workspace/rnaseq/de/htseq_counts/ENSG_ID2Name.txt", header=TRUE, stringsAsFactors=FALSE)
 colnames(gene_names)=c("gene_id","gene_name")
 
 #Import DE results from the HISAT2/htseq-count/DESeq2 pipeline (http://genomedata.org/cri-workshop/deseq2/DE_all_genes_DESeq2.tsv)
 setwd(outdir)
-results_genes <-read.table("DE_all_genes_DESeq2.tsv", sep="\t", header=T, stringsAsFactors = F)
+results_genes <-read.table("~/workspace/rnaseq/de/deseq2/DE_all_genes_DESeq2.tsv", sep="\t", header=T, stringsAsFactors = F)
 
 ```
 

diff --git a/_posts/0003-05-01-DE_Pathway_Analysis.md b/_posts/0003-05-01-DE_Pathway_Analysis.md
@@ -32,8 +32,8 @@ Before we perform the pathway analysis we need to read in our differential expre
 ```R
 
 #Define working dir paths
-datadir = "/cloud/project/outdir"
-#datadir = "~/workspace/rnaseq/de/htseq_counts/"
+# datadir = "/cloud/project/outdir"
+datadir = "~/workspace/rnaseq/de/deseq2/"
 
 setwd(datadir)
 

diff --git a/_posts/0003-06-02-Batch-Correction.md b/_posts/0003-06-02-Batch-Correction.md
@@ -64,10 +64,15 @@ Perform the following analyses in `R`:
 ```R
 
 #Define working dir paths
-datadir = "/cloud/project/data/bulk_rna"
-#datadir = "~/workspace/rnaseq/batch_correction"
+# datadir = "/cloud/project/data/bulk_rna"
+# outdir = "/cloud/project/outdir"
+
+datadir = "~/workspace/rnaseq/batch_correction"
+outdir = "~/workspace/rnaseq/batch_correction/outputs"
+
+if (!dir.exists(outdir)) dir.create(outdir)
+
 
-outdir = "/cloud/project/outdir"
 
 #load neccessary libraries
 library("sva") #Note this exercise requires sva (>= v3.36.0) which is only available for R (>= v4.x)