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Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Cmd+Shift+Enter.
setwd("~/Documents/RobertsLab/Hollie-Geoduck/Macau2")
## Reads in some of the sample files, it also changes any "." characters to NAs.
EPI_111_CG <- read_delim("~/Documents/RobertsLab/Hollie-Geoduck/Merge-test/VCF-Test/EPI-111-CG.output", "\t", escape_double = FALSE, trim_ws = TRUE, na = ".")Parsed with column specification:
cols(
`#CHROM` = col_character(),
POS = col_integer(),
CONTEXT = col_character(),
`Watson METH` = col_integer(),
`Watson COVERAGE` = col_integer(),
`Watson QUAL` = col_integer(),
`Crick METH` = col_integer(),
`Crick COVERAGE` = col_integer(),
`Crick QUAL` = col_integer()
)EPI_113_CG <- read_delim("~/Documents/RobertsLab/Hollie-Geoduck/Merge-test/VCF-Test/EPI-113-CG.output", "\t", escape_double = FALSE, trim_ws = TRUE, na = ".")Parsed with column specification:
cols(
`#CHROM` = col_character(),
POS = col_integer(),
CONTEXT = col_character(),
`Watson METH` = col_integer(),
`Watson COVERAGE` = col_integer(),
`Watson QUAL` = col_integer(),
`Crick METH` = col_integer(),
`Crick COVERAGE` = col_integer(),
`Crick QUAL` = col_integer()
)
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|================================================================================| 100% 55 MBEPI_104_CG <- read_delim("~/Documents/RobertsLab/Hollie-Geoduck/Merge-test/VCF-Test/EPI-104-CG.output", "\t", escape_double = FALSE, trim_ws = TRUE, na = ".")Parsed with column specification:
cols(
`#CHROM` = col_character(),
POS = col_integer(),
CONTEXT = col_character(),
`Watson METH` = col_integer(),
`Watson COVERAGE` = col_integer(),
`Watson QUAL` = col_integer(),
`Crick METH` = col_integer(),
`Crick COVERAGE` = col_integer(),
`Crick QUAL` = col_integer()
)
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|================================================================================| 100% 70 MBEPI_119_CG <- read_delim("~/Documents/RobertsLab/Hollie-Geoduck/Merge-test/VCF-Test/EPI-119-CG.output", "\t", escape_double = FALSE, trim_ws = TRUE, na = ".")Parsed with column specification:
cols(
`#CHROM` = col_character(),
POS = col_integer(),
CONTEXT = col_character(),
`Watson METH` = col_integer(),
`Watson COVERAGE` = col_integer(),
`Watson QUAL` = col_integer(),
`Crick METH` = col_integer(),
`Crick COVERAGE` = col_integer(),
`Crick QUAL` = col_integer()
)## Sums the meth and coverage columns between both strands, since MethExtract outputs them separate
EPI_104_CG[,10] <- rowSums(cbind(EPI_104_CG$`Watson METH`, EPI_104_CG$`Crick METH`), na.rm = TRUE)
EPI_104_CG[,11] <- rowSums(cbind(EPI_104_CG$`Watson COVERAGE`, EPI_104_CG$`Crick COVERAGE`), na.rm = TRUE)
EPI_104_CG[,12] <- "EPI_104"
EPI_111_CG[,10] <- rowSums(cbind(EPI_111_CG$`Watson METH`, EPI_111_CG$`Crick METH`), na.rm = TRUE)
EPI_111_CG[,11] <- rowSums(cbind(EPI_111_CG$`Watson COVERAGE`, EPI_111_CG$`Crick COVERAGE`), na.rm = TRUE)
EPI_111_CG[,12] <- "EPI_111"
EPI_113_CG[,10] <- rowSums(cbind(EPI_113_CG$`Watson METH`, EPI_113_CG$`Crick METH`), na.rm = TRUE)
EPI_113_CG[,11] <- rowSums(cbind(EPI_113_CG$`Watson COVERAGE`, EPI_113_CG$`Crick COVERAGE`), na.rm = TRUE)
EPI_113_CG[,12] <- "EPI_113"
EPI_119_CG[,10] <- rowSums(cbind(EPI_119_CG$`Watson METH`, EPI_119_CG$`Crick METH`), na.rm = TRUE)
EPI_119_CG[,11] <- rowSums(cbind(EPI_119_CG$`Watson COVERAGE`, EPI_119_CG$`Crick COVERAGE`), na.rm = TRUE)
EPI_119_CG[,12] <- "EPI_119"
## Names the columns
colnames(EPI_104_CG)[10:12] <- c("TotalMeth104", "TotalCov104", "SampleName")
colnames(EPI_111_CG)[10:12] <- c("TotalMeth111", "TotalCov111", "SampleName")
colnames(EPI_113_CG)[10:12] <- c("TotalMeth113", "TotalCov113", "SampleName")
colnames(EPI_119_CG)[10:12] <- c("TotalMeth119", "TotalCov119", "SampleName")
## Merges the different samples into a single file. the merge() function in R only allows two data frames to be merged at a time, so they
## have to be done sequentially. A more efficient soltuion will probably need to be found prior to analyzing the full sample set
methylated.1 <- merge(EPI_104_CG[,c(1, 2, 3, 10)], EPI_111_CG[,c(1, 2, 3, 10)], by = names(EPI_111_CG[,c(1,2,3)]), all = T)
methylated.2 <- merge(methylated.1, EPI_113_CG[,c(1, 2, 3, 10)], all = T)
methylated.3 <- merge(methylated.2, EPI_119_CG[,c(1, 2, 3, 10)], all = T)
total.cov1 <- merge(EPI_104_CG[,c(1, 2, 3, 11)], EPI_111_CG[,c(1, 2, 3, 11)], by = names(EPI_111_CG[,c(1,2,3)]), all = T)
total.cov2 <- merge(total.cov1, EPI_113_CG[,c(1, 2, 3, 11)], all = T)
total.cov3 <- merge(total.cov2, EPI_119_CG[,c(1, 2, 3, 11)], all = T)
head(methylated.3)head(total.cov3)EPI104.total <- as.data.frame(cbind(total.cov3[,1], total.cov3[,2], total.cov3[,2]))
EPI104.total[,4] <- methylated.3[,4] / total.cov3[,4]
EPI111.total <- as.data.frame(cbind(total.cov3[,1], total.cov3[,2], total.cov3[,2]))
EPI111.total[,4] <- methylated.3[,5] / total.cov3[,5]
EPI113.total <- as.data.frame(cbind(total.cov3[,1], total.cov3[,2], total.cov3[,2]))
EPI113.total[,4] <- methylated.3[,6] / total.cov3[,6]
EPI119.total <- as.data.frame(cbind(total.cov3[,1], total.cov3[,2], total.cov3[,2]))
EPI119.total[,4] <- methylated.3[,7] / total.cov3[,7]
write.table(EPI104.total, file = "EPI-104-Total-Methylation.bedgraph", sep = "\t", col.names = FALSE, row.names = FALSE, quote = FALSE, na = "0")
write.table(EPI111.total, file = "EPI-111-Total-Methylation.bedgraph", sep = "\t", col.names = FALSE, row.names = FALSE, quote = FALSE, na = "0")
write.table(EPI113.total, file = "EPI-113-Total-Methylation.bedgraph", sep = "\t", col.names = FALSE, row.names = FALSE, quote = FALSE, na = "0")
write.table(EPI119.total, file = "EPI-119-Total-Methylation.bedgraph", sep = "\t", col.names = FALSE, row.names = FALSE, quote = FALSE, na = "0")## Trims the combined data set of all non-complete rows (If any sample has an NA at a loci, that loci is removed)
methylated.3[complete.cases(methylated.3[, c(4,5,6,7)]),] -> macau.meth4
## Trims the combined data set of any loci that doesn't have at least 10x coverage at each site.
macau.meth5 <- macau.meth4[apply(macau.meth4[, c(4,5,6,7)], MARGIN = 1, function(x) all(x > 10)), ]
total.cov3[complete.cases(total.cov3[, c(4,5,6,7)]),] -> macau.total4
macau.total5 <- macau.total4[apply(macau.total4[, c(4,5,6,7)], MARGIN = 1, function(x) all(x > 10)), ]
head(macau.meth5)head(macau.total5)## Makes a concatenated scaffold/loci label
macau.meth5[,8] <- paste0(macau.meth5[,1], "-", macau.meth5[,2])
macau.total5[,8] <- paste0(macau.total5[,1], "-", macau.total5[,2])
## Removes all loci present in the total coverage file, but not in the methylation file.
macau.total6 <- macau.total5[macau.total5[,8] %in% macau.meth5[,8],]
## Creates the final column for Macau input, with labels, then writes them to white-space separated files.
macau.meth6 <- cbind(macau.meth5[,8], macau.meth5[,4], macau.meth5[,5], macau.meth5[,6], macau.meth5[,7])
colnames(macau.meth6) <- c("loc", "EPI-104", "EPI-111", "EPI-113", "EPI-119")
macau.total7 <- cbind(macau.total6[,8], macau.total6[,4], macau.total6[,5], macau.total6[,6], macau.total6[,7])
colnames(macau.total7) <- c("loc", "EPI-104", "EPI-111", "EPI-113", "EPI-119")
## Writes out the macau methylation and coverage files
write.table(macau.meth6, file = "macau.meth.txt", sep = " ", quote = FALSE, row.names = FALSE)
write.table(macau.total7, file = "macau.totalcov.txt", sep = " ", quote = FALSE, row.names = FALSE)result_assoc <- read_delim("~/Documents/RobertsLab/Hollie-Geoduck/Macau2/results.txt",
"\t", escape_double = FALSE, trim_ws = TRUE)Parsed with column specification:
cols(
id = col_character(),
n = col_integer(),
acpt_rate = col_double(),
beta = col_double(),
se_beta = col_double(),
pvalue = col_double(),
h = col_double(),
se_h = col_double(),
sigma2 = col_double(),
se_sigma2 = col_double(),
alpha0 = col_double(),
se_alpha0 = col_double()
)## Removes all regions with associated p-values greater than 0.05
sig.results <- result_assoc[result_assoc$pvalue <= 0.05,]
## Splits the Scaffold # and location # apart using the "-" character between them ad then saves it to colums 13 and 14
for(i in 1:nrow(sig.results)) {
temp <- strsplit(sig.results$id[i], "-")
sig.results[i,13] <- temp[[1]][1]
sig.results[i,14] <- temp[[1]][2]
}
colnames(sig.results)[c(13,14)] <- c("Scaffold", "Loc")
## Pulls out the scaffold name, location, and h values associated with all significant DMRs
bed.test <- as.data.frame(cbind(sig.results[,13], (sig.results[,14]), (sig.results[,14]), sig.results$h))
colnames(bed.test)[4] <- "h"
write.table(bed.test, file = "DiffMethRegions.bed", sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE)Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Cmd+Option+I.
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