Commit 56b68b89 authored by Venkat Malladi's avatar Venkat Malladi

update p-value analysis for mcf-7 and AC16.

parent f4d4e766
...@@ -318,6 +318,12 @@ dev.off() ...@@ -318,6 +318,12 @@ dev.off()
boundTesting <-matrix(c(952,5471,205,239),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("mRNA", "snoRNA"))) boundTesting <-matrix(c(952,5471,205,239),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("mRNA", "snoRNA")))
fisher.test(boundTesting) fisher.test(boundTesting)
boundTesting <-matrix(c(2461,7406,205,239),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("lncRNA", "snoRNA")))
fisher.test(boundTesting)
boundTesting <-matrix(c(284,199,205,239),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("snRNA", "snoRNA")))
fisher.test(boundTesting)
# Boxplot of Preimmune vs PARP-1 (C) # Boxplot of Preimmune vs PARP-1 (C)
jpeg('boxplot-mcf-7-basal-species.jpg') jpeg('boxplot-mcf-7-basal-species.jpg')
boxplot(MLK_RIP_sno_rpkm,col=(c("orange","blue")),outline=FALSE,ylim = c(0,400),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1) boxplot(MLK_RIP_sno_rpkm,col=(c("orange","blue")),outline=FALSE,ylim = c(0,400),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1)
...@@ -400,6 +406,12 @@ dev.off() ...@@ -400,6 +406,12 @@ dev.off()
typeTesting <-matrix(c(63,19,38,76),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "CD"))) typeTesting <-matrix(c(63,19,38,76),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "CD")))
fisher.test(typeTesting) fisher.test(typeTesting)
typeTesting <-matrix(c(63,19,85,199),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "snRNA")))
fisher.test(typeTesting)
typeTesting <-matrix(c(63,19,15,4),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "scRNA")))
fisher.test(typeTesting)
# Combine snRNA and snoRNA and print out # Combine snRNA and snoRNA and print out
allsnotx <- data.frame(seqnames=seqnames(allsno), allsnotx <- data.frame(seqnames=seqnames(allsno),
starts=start(allsno)-1, starts=start(allsno)-1,
...@@ -997,7 +1009,13 @@ ratios <- c(pc_ratio,lnc_ratio,sno_ratio,sn_ratio) ...@@ -997,7 +1009,13 @@ ratios <- c(pc_ratio,lnc_ratio,sno_ratio,sn_ratio)
barplot(ratios, main="SNORNA AC16", col=c("red","black", "dimgrey", "lightgrey"),ylim=c(0,.5)) barplot(ratios, main="SNORNA AC16", col=c("red","black", "dimgrey", "lightgrey"),ylim=c(0,.5))
dev.off() dev.off()
boundTesting <-matrix(c(68,6619,84,319),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("mRNA", "snoRNA"))) boundTesting <-matrix(c(68,6619,184,319),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("mRNA", "snoRNA")))
fisher.test(boundTesting)
boundTesting <-matrix(c(1159,8796,184,319),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("lncRNA", "snoRNA")))
fisher.test(boundTesting)
boundTesting <-matrix(c(76,239,184,319),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("mRNA", "snoRNA")))
fisher.test(boundTesting) fisher.test(boundTesting)
# Boxplot of Preimmune vs PARP-1 (C) # Boxplot of Preimmune vs PARP-1 (C)
...@@ -1081,6 +1099,12 @@ dev.off() ...@@ -1081,6 +1099,12 @@ dev.off()
typeTesting <-matrix(c(50,28,49,115),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "CD"))) typeTesting <-matrix(c(50,28,49,115),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "CD")))
fisher.test(typeTesting) fisher.test(typeTesting)
typeTesting <-matrix(c(50,28,76,239),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "snRNA")))
fisher.test(typeTesting)
typeTesting <-matrix(c(50,28,7,13),nrow = 2,dimnames = list(Guess = c("bound", "unbound"),Truth = c("HA", "scRNA")))
fisher.test(typeTesting)
# Combine snRNA and snoRNA and print out # Combine snRNA and snoRNA and print out
allsnotx_a <- data.frame(seqnames=seqnames(alk_allsno), allsnotx_a <- data.frame(seqnames=seqnames(alk_allsno),
starts=start(alk_allsno)-1, starts=start(alk_allsno)-1,
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment