/
Find_Replication_Origin.R
executable file
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/
Find_Replication_Origin.R
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if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("rnaseqWrapper", "seqinr","DESeq","topGO"))
BiocManager::install(c("argparse"))
?BiocManager
oriloc_1 <- seqinr::oriloc(seq.fasta = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece1.fasta",
g2.coord = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece1.predict",
glimmer.version = 3,
oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)
oriloc_1
# system.file("/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece1.fasta",
# package = "seqinr")
# system.file(""/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece1.predict",
# package = "seqinr")
oriloc_2 <- seqinr::oriloc(seq.fasta = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece2.fasta",
g2.coord = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece2.predict",
glimmer.version = 3,
oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)
oriloc_3 <- seqinr::oriloc(seq.fasta = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece3.fasta",
g2.coord = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece3.predict",
glimmer.version = 3,
oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)
oriloc_4 <- seqinr::oriloc(seq.fasta = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece2.fasta",
g2.coord = "/Users/jerrypan/Desktop/GRIPS/Analysis/20190722-glimmer/GCF_000027085.1_ASM2708v1_genomic_piece2.predict",
glimmer.version = 3,
oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)
seqinr::draw.oriloc(oriloc_1,main = "Nucleotide skews in chromosomes",
xlab = "Genomic Location (Mbp)", ylab = "Coverage (# reads)",
las = 1, las.right = 3,
ta.mtext = "Cumul. T-A skew", ta.col = "pink", ta.lwd = 1,
cg.mtext = "Cumul. C-G skew", cg.col = "lightblue", cg.lwd = 1,
cds.mtext = "Cumul. CDS skew", cds.col = "lightgreen", cds.lwd = 1,
sk.col = "black", sk.lwd = 2,
add.grid = TRUE)