Commit 85d806b8 authored by Venkat Malladi's avatar Venkat Malladi

Add in stage analysis.

parent 6f3c7a03
......@@ -153,7 +153,7 @@ dev.off()
parp1_pam.aov = aov(PARP1 ~ PAM,data=df_pd_tcag_gtex_pam)
summary(parp1_pam.aov)
## PHF8 and PAM
## DDX21 and PAM
df_ddx21_PAM_tcag_gtex_summary <- summarySE(df_pd_tcag_gtex_pam, measurevar="DDX21", groupvars=c("PAM"))
p <- ggplot(df_ddx21_PAM_tcag_gtex_summary, aes(x = as.factor(PAM), fill= PAM)) +
geom_boxplot(aes(
......@@ -263,3 +263,51 @@ dev.off()
ddx21_type.aov = aov(DDX21 ~ Type,data=df_et_tcag_type)
summary(ddx21_type.aov)
### Stage TCGA
pd_tcga_breast_stage <- pd_tcga_breast[complete.cases(pd_tcga_breast[ , 4]),]
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IA'] <- 'Stage I'
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IB'] <- 'Stage I'
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IIA'] <- 'Stage II'
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IIB'] <- 'Stage II'
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IIIA'] <- 'Stage III'
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IIIB'] <- 'Stage III'
pd_tcga_breast_stage$Stage[pd_tcga_breast_stage$Stage == 'Stage IIIC'] <- 'Stage III'
pd_tcga_breast_stage_known <- pd_tcga_breast_stage[ ! pd_tcga_breast_stage$Stage %in% c('Stage Tis','Stage X'), ]
pd_tcga_breast_stage_known$PARP1 <- log2(pd_tcga_breast_stage_known$PARP1)
pd_tcga_breast_stage_known$DDX21 <- log2(pd_tcga_breast_stage_known$DDX21)
## PARP1 and Stage
df_tcga_parp1_stage <- summarySE(pd_tcga_breast_stage_known, measurevar="PARP1", groupvars=c("Stage"))
p <- ggplot(df_tcga_parp1_stage, aes(x = as.factor(Stage), fill= Stage)) +
geom_boxplot(aes(
lower = PARP1 - se,
upper = PARP1 + se,
middle = PARP1,
ymin = PARP1 - 2*se,
ymax = PARP1 + 2*se),
stat = "identity",lwd=1.5) + geom_hline(yintercept = mean(pd_tcga_breast_stage_known$PARP1), linetype = 2) + labs(y="RPKM",x="PARP1") + theme_bw() + theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.ticks=element_line(size=1))
jpeg('figures/PARP1_breast_correlation_stage_boxplot.jpg')
p
dev.off()
parp1_stage.aov = aov(PARP1 ~ Stage ,data=pd_tcga_breast_stage_known)
summary(parp1_stage.aov)
## DDX21 and Stage
df_tcga_ddx21_stage <- summarySE(pd_tcga_breast_stage_known, measurevar="DDX21", groupvars=c("Stage"))
p <- ggplot(df_tcga_ddx21_stage, aes(x = as.factor(Stage), fill= Stage)) +
geom_boxplot(aes(
lower = DDX21 - se,
upper = DDX21 + se,
middle = DDX21,
ymin = DDX21 - 2*se,
ymax = DDX21 + 2*se),
stat = "identity",lwd=1.5) + geom_hline(yintercept = mean(pd_tcga_breast_stage_known$DDX21), linetype = 2) + labs(y="RPKM",x="DDX21") + theme_bw() + theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.ticks=element_line(size=1))
jpeg('figures/DDX21_breast_correlation_stage_boxplot.jpg')
p
dev.off()
ddx21_stage.aov = aov(DDX21 ~ Stage,data=pd_tcga_breast_stage_known)
summary(ddx21_stage.aov)
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