library(CircTest)
Circ <- read.delim('Circ.csv', header = T, as.is = T)
Linear <- read.delim('Linear.csv', header = T, as.is = T)
CircCoord <- read.delim('CircCoordinates.csv', header = T, as.is = T)
Circ
# CircID Chr Start End Control_1 Control_2 Control_3 Treatment_1 Treatment_2 Treatment_3
# 1 chr1:100|800 chr1 100 800 0 2 1 5 4 0
# 2 chr1:1050|10080 chr1 1050 10080 20 22 21 10 13 0
# 3 chr2:600|1000 chr2 600 1000 0 1 0 10 0 1
# 4 chr10:4100|5400 chr10 4100 5400 55 54 52 56 53 50
# 5 chr11:600|1500 chr11 600 1500 3 0 1 2 2 3
Linear
# CircID Chr Start End Control_1 Control_2 Control_3 Treatment_1 Treatment_2 Treatment_3
# 1 chr1:100|800 chr1 100 800 10 11 12 9 10 10
# 2 chr1:1050|10080 chr1 1050 10080 80 81 83 45 48 46
# 3 chr2: 600|1000 chr2 600 1000 5 5 2 12 8 7
# 4 chr10:4100|5400 chr10 4100 5400 101 110 106 150 160 153
# 5 chr11:600|1500 chr11 600 1500 20 21 18 19 20 20
CircCoord
# CircID Chr Start End Gene
# 1 chr1:100|800 chr1 100 800 Gene_A
# 2 chr1:1050|10080 chr1 1050 10080 Gene_B
# 3 chr2: 600|1000 chr2 600 1000 Gene_C
# 4 chr10:4100|5400 chr10 4100 5400 Gene_D
# 5 chr11:600|1500 chr11 600 1500 Gene_E
Circ_filtered <- Circ.filter(circ = Circ, linear = Linear, Nreplicates = 3, filter.sample = 3, filter.count = 5, percentage = 0.1, circle_description = c(1:4))
Linear_filtered <- Linear[rownames(Circ_filtered),]
CircCoord_filtered <- CircCoord[rownames(Circ_filtered),]
Circ_filtered
# CircID Chr Start End Control_1 Control_2 Control_3 Treatment_1 Treatment_2 Treatment_3
# 2 chr1:1050|10080 chr1 1050 10080 20 22 21 10 13 0
# 4 chr10:4100|5400 chr10 4100 5400 55 54 52 56 53 50
Linear_filtered
# CircID Chr Start End Control_1 Control_2 Control_3 Treatment_1 Treatment_2 Treatment_3
# 2 chr1:1050|10080 chr1 1050 10080 80 81 83 45 48 46
# 4 chr10:4100|5400 chr10 4100 5400 101 110 106 150 160 153
CircCoord_filtered
# CircID Chr Start End Gene
# 2 chr1:1050|10080 chr1 1050 10080 Gene_B
# 4 chr10:4100|5400 chr10 4100 5400 Gene_D
test <- Circ.test(Circ_filtered, Linear_filtered, CircCoord_filtered, group=c(rep(1,3),rep(2,3)), circle_description = c(1:4))
# $summary_table
# CircID Chr Start End Gene sig_p
# 4 chr10:4100|5400 chr10 4100 5400 Gene_D 0.01747407
#
# $sig.dat
# CircID Chr Start End Control_1 Control_2 Control_3 Treatment_1 Treatment_2 Treatment_3
# 4 chr10:4100|5400 chr10 4100 5400 55 54 52 56 53 50
#
# $p.val
# [1] 0.153464107 0.008737037
#
# $p.adj
# [1] 0.15346411 0.01747407
#
# $sig_p
# [1] 0.01747407
#
pdf('example_pictures.pdf')
for (i in rownames(test$summary_table)) {
Circ.ratioplot(Circ_filtered, Linear_filtered, CircCoord_filtered, plotrow=i, groupindicator1=c(rep('Control',3),rep('Treatment',3)),
lab_legend='Condition', circle_description = c(1:4), gene_column = 5 )
}
for (i in rownames(test$summary_table)) {
Circ.lineplot(Circ_filtered, Linear_filtered, CircCoord_filtered, plotrow=i, groupindicator1=c(rep('Control',3),rep('Treatment',3)),
circle_description = c(1:4), gene_column = 5 )
}
dev.off()
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