Commit 4ad9198e authored by Venkat Malladi's avatar Venkat Malladi

Update analysis.

parent 811feb75
...@@ -8,6 +8,7 @@ biocLite("groHMM") ...@@ -8,6 +8,7 @@ biocLite("groHMM")
biocLite("org.Hs.eg.db") biocLite("org.Hs.eg.db")
biocLite("edgeR") biocLite("edgeR")
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
biocLite("BSgenome.Hsapiens.UCSC.hg19")
biocLite("goseq") biocLite("goseq")
install.packages("ggplot2") install.packages("ggplot2")
install.packages("VennDiagram") install.packages("VennDiagram")
...@@ -21,6 +22,7 @@ library(GenomicFeatures) ...@@ -21,6 +22,7 @@ library(GenomicFeatures)
library(ggplot2) library(ggplot2)
library(VennDiagram) library(VennDiagram)
library(reshape) library(reshape)
library(BSgenome.Hsapiens.UCSC.hg19)
``` ```
## Functions ## Functions
...@@ -475,8 +477,14 @@ wilcox.test(MPK_enrichment[,1], MPK_enrichment[,2],paired=T) ...@@ -475,8 +477,14 @@ wilcox.test(MPK_enrichment[,1], MPK_enrichment[,2],paired=T)
``` ```
```{r alignments Estrogen} ```{r alignments Estrogen}
MLKE_RNA1 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RNAseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RNA1/align-star-se.sh-1.0.0/MLKE_RNA1_AGTTCC_L008_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
MLKE_RNA2 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RNAseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RNA2/align-star-se.sh-1.0.0/MLKE_RNA2_GTGAAA_L008_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
MLKE_RIP_PI1 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PI/align-star-se.sh-2.0.0/MLKE_RIP1_PI_CAGATC_L006_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
MLKE_RIP_PI2 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PI/align-star-se.sh-2.0.0/MLKE_RIP2_PI_GAGTGG_L008_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
MLKE_RIP_PARP1 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PARP1_SecondRun/align-star-se.sh-2.0.0/MLKE_RIP1_PARP1_ACTTGA_L004_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
MLKE_RIP_PARP2 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PARP1_16/align-star-se.sh-2.0.0/MLKE_RIP2_PARP1_16_CCGTCC_L007_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
``` ```
```{r counts Estrogen} ```{r counts Estrogen}
...@@ -753,6 +761,7 @@ write.table(mlke_allsnotx_rna_rpkm, file="mcf-7-e2-snRNA_RPKM_RNA.tsv", quote=F, ...@@ -753,6 +761,7 @@ write.table(mlke_allsnotx_rna_rpkm, file="mcf-7-e2-snRNA_RPKM_RNA.tsv", quote=F,
``` ```
# Overlap of snoRNA and snRNA # Overlap of snoRNA and snRNA
``` {r snoRNA Overlap} ``` {r snoRNA Overlap}
......
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