Commit a1d1bfe8 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Naive assembly

parent f723c65c
......@@ -146,7 +146,7 @@ for(i in seq_along(samples)){
assign(paste(samples[i], "_quast", sep=""), dat )
rm(dat, dat1, dat2)
#rm(dat, dat1, dat2)
}
assm_mgmt <- c("IMP","IMP-megahit","MOCAT_MGMT","MetAmos_MGMT")
......
......@@ -66,6 +66,22 @@ for(i in seq_along(samples)){
))
}
## MG data usage of naive assembly
for(i in seq_along(samples)){
assign(paste(samples[i], "_MG_x_naive", sep=""),
read.flagstat(
paste(indir.flagstat, "/", samples[i], "/", "naive_assmebly", "/", "MG_IMP_x_MG_MT_cap3.merged.sorted_flagstat.txt", sep="")
))
}
## MT data usage of naive assembly
for(i in seq_along(samples)){
assign(paste(samples[i], "_MT_x_naive", sep=""),
read.flagstat(
paste(indir.flagstat, "/", samples[i], "/", "naive_assmebly", "/", "MT_IMP_x_MG_MT_cap3.merged.sorted_flagstat.txt", sep="")
))
}
## MG data usage of IMP-MG
for(i in seq_along(samples)){
assign(paste(samples[i], "_IMP_MG_x_MG", sep=""),
......@@ -203,7 +219,7 @@ for(i in seq_along(samples)){
}
assms <- c("IMP", "IMP-megahit", "MOCAT_MGMT", "MetAmos_MGMT", "IMP_MG", "MOCAT_MG", "MetAmos_MG", "IMP_MT", "MOCAT_MT", "MetAmos_MT")
assms <- c("IMP", "IMP-megahit", "naive", "MOCAT_MGMT", "MetAmos_MGMT", "IMP_MG", "MOCAT_MG", "MetAmos_MG", "IMP_MT", "MOCAT_MT", "MetAmos_MT")
#####################################################################################################################################
### SM data summary
......@@ -216,6 +232,7 @@ rbind.data.frame(
c(
SM_IMP_MG_x_MGMT$fraction[3],
get("SM_IMP-megahit_MG_x_MGMT")$fraction[3],
SM_MG_x_naive$fraction[3],
SM_MOCAT_MG_x_MGMT$fraction[3],
SM_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -232,6 +249,7 @@ rbind.data.frame(
c(
SM_IMP_MG_x_MGMT$fraction[7],
get("SM_IMP-megahit_MG_x_MGMT")$fraction[7],
SM_MG_x_naive$fraction[7],
SM_MOCAT_MG_x_MGMT$fraction[7],
SM_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -248,6 +266,7 @@ rbind.data.frame(
c(
SM_IMP_MT_x_MGMT$fraction[3],
get("SM_IMP-megahit_MT_x_MGMT")$fraction[3],
SM_MT_x_naive$fraction[3],
SM_MOCAT_MT_x_MGMT$fraction[3],
SM_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -264,6 +283,7 @@ rbind.data.frame(
c(
SM_IMP_MT_x_MGMT$fraction[7],
get("SM_IMP-megahit_MT_x_MGMT")$fraction[7],
SM_MT_x_naive$fraction[7],
SM_MOCAT_MT_x_MGMT$fraction[7],
SM_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -279,6 +299,7 @@ rbind.data.frame(
)
colnames(SM.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
SM.reads <- cbind(Dataset=rep("SM", nrow(SM.reads)), SM.reads)
#####################################################################################################################################
### HF1 data summary
......@@ -291,6 +312,7 @@ rbind.data.frame(
c(
HF1_IMP_MG_x_MGMT$fraction[3],
get("HF1_IMP-megahit_MG_x_MGMT")$fraction[3],
HF1_MG_x_naive$fraction[3],
HF1_MOCAT_MG_x_MGMT$fraction[3],
HF1_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -307,6 +329,7 @@ rbind.data.frame(
c(
HF1_IMP_MG_x_MGMT$fraction[7],
get("HF1_IMP-megahit_MG_x_MGMT")$fraction[7],
HF1_MG_x_naive$fraction[7],
HF1_MOCAT_MG_x_MGMT$fraction[7],
HF1_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -323,6 +346,7 @@ rbind.data.frame(
c(
HF1_IMP_MT_x_MGMT$fraction[3],
get("HF1_IMP-megahit_MT_x_MGMT")$fraction[3],
HF1_MT_x_naive$fraction[3],
HF1_MOCAT_MT_x_MGMT$fraction[3],
HF1_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -339,6 +363,7 @@ rbind.data.frame(
c(
HF1_IMP_MT_x_MGMT$fraction[7],
get("HF1_IMP-megahit_MT_x_MGMT")$fraction[7],
HF1_MT_x_naive$fraction[7],
HF1_MOCAT_MT_x_MGMT$fraction[7],
HF1_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -354,6 +379,7 @@ rbind.data.frame(
)
colnames(HF1.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
HF1.reads <- cbind(Dataset=rep("HF1", nrow(HF1.reads)), HF1.reads)
#####################################################################################################################################
### HF2 data summary
......@@ -366,6 +392,7 @@ rbind.data.frame(
c(
HF2_IMP_MG_x_MGMT$fraction[3],
get("HF2_IMP-megahit_MG_x_MGMT")$fraction[3],
HF2_MG_x_naive$fraction[3],
HF2_MOCAT_MG_x_MGMT$fraction[3],
HF2_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -382,6 +409,7 @@ rbind.data.frame(
c(
HF2_IMP_MG_x_MGMT$fraction[7],
get("HF2_IMP-megahit_MG_x_MGMT")$fraction[7],
HF2_MG_x_naive$fraction[7],
HF2_MOCAT_MG_x_MGMT$fraction[7],
HF2_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -398,6 +426,7 @@ rbind.data.frame(
c(
HF2_IMP_MT_x_MGMT$fraction[3],
get("HF2_IMP-megahit_MT_x_MGMT")$fraction[3],
HF2_MT_x_naive$fraction[3],
HF2_MOCAT_MT_x_MGMT$fraction[3],
HF2_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -414,6 +443,7 @@ rbind.data.frame(
c(
HF2_IMP_MT_x_MGMT$fraction[7],
get("HF2_IMP-megahit_MT_x_MGMT")$fraction[7],
HF2_MT_x_naive$fraction[7],
HF2_MOCAT_MT_x_MGMT$fraction[7],
HF2_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -429,6 +459,7 @@ rbind.data.frame(
)
colnames(HF2.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
HF2.reads <- cbind(Dataset=rep("HF2", nrow(HF2.reads)), HF2.reads)
#####################################################################################################################################
### HF3 data summary
......@@ -441,6 +472,7 @@ rbind.data.frame(
c(
HF3_IMP_MG_x_MGMT$fraction[3],
get("HF3_IMP-megahit_MG_x_MGMT")$fraction[3],
HF3_MG_x_naive$fraction[3],
HF3_MOCAT_MG_x_MGMT$fraction[3],
HF3_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -457,6 +489,7 @@ rbind.data.frame(
c(
HF3_IMP_MG_x_MGMT$fraction[7],
get("HF3_IMP-megahit_MG_x_MGMT")$fraction[7],
HF3_MG_x_naive$fraction[7],
HF3_MOCAT_MG_x_MGMT$fraction[7],
HF3_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -473,6 +506,7 @@ rbind.data.frame(
c(
HF3_IMP_MT_x_MGMT$fraction[3],
get("HF3_IMP-megahit_MT_x_MGMT")$fraction[3],
HF3_MT_x_naive$fraction[3],
HF3_MOCAT_MT_x_MGMT$fraction[3],
HF3_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -489,6 +523,7 @@ rbind.data.frame(
c(
HF3_IMP_MT_x_MGMT$fraction[7],
get("HF3_IMP-megahit_MT_x_MGMT")$fraction[7],
HF3_MT_x_naive$fraction[7],
HF3_MOCAT_MT_x_MGMT$fraction[7],
HF3_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -504,6 +539,7 @@ rbind.data.frame(
)
colnames(HF3.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
HF3.reads <- cbind(Dataset=rep("HF3", nrow(HF3.reads)), HF3.reads)
#####################################################################################################################################
### HF4 data summary
......@@ -516,6 +552,7 @@ rbind.data.frame(
c(
HF4_IMP_MG_x_MGMT$fraction[3],
get("HF4_IMP-megahit_MG_x_MGMT")$fraction[3],
HF4_MG_x_naive$fraction[3],
HF4_MOCAT_MG_x_MGMT$fraction[3],
HF4_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -532,6 +569,7 @@ rbind.data.frame(
c(
HF4_IMP_MG_x_MGMT$fraction[7],
get("HF4_IMP-megahit_MG_x_MGMT")$fraction[7],
HF4_MG_x_naive$fraction[7],
HF4_MOCAT_MG_x_MGMT$fraction[7],
HF4_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -548,6 +586,7 @@ rbind.data.frame(
c(
HF4_IMP_MT_x_MGMT$fraction[3],
get("HF4_IMP-megahit_MT_x_MGMT")$fraction[3],
HF4_MT_x_naive$fraction[3],
HF4_MOCAT_MT_x_MGMT$fraction[3],
HF4_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -564,6 +603,7 @@ rbind.data.frame(
c(
HF4_IMP_MT_x_MGMT$fraction[7],
get("HF4_IMP-megahit_MT_x_MGMT")$fraction[7],
HF4_MT_x_naive$fraction[7],
HF4_MOCAT_MT_x_MGMT$fraction[7],
HF4_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -579,6 +619,8 @@ rbind.data.frame(
)
colnames(HF4.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
HF4.reads <- cbind(Dataset=rep("HF4", nrow(HF4.reads)), HF4.reads)
#####################################################################################################################################
### HF5 data summary
......@@ -591,6 +633,7 @@ rbind.data.frame(
c(
HF5_IMP_MG_x_MGMT$fraction[3],
get("HF5_IMP-megahit_MG_x_MGMT")$fraction[3],
HF5_MG_x_naive$fraction[3],
HF5_MOCAT_MG_x_MGMT$fraction[3],
HF5_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -607,6 +650,7 @@ rbind.data.frame(
c(
HF5_IMP_MG_x_MGMT$fraction[7],
get("HF5_IMP-megahit_MG_x_MGMT")$fraction[7],
HF5_MG_x_naive$fraction[7],
HF5_MOCAT_MG_x_MGMT$fraction[7],
HF5_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -623,6 +667,7 @@ rbind.data.frame(
c(
HF5_IMP_MT_x_MGMT$fraction[3],
get("HF5_IMP-megahit_MT_x_MGMT")$fraction[3],
HF5_MT_x_naive$fraction[3],
HF5_MOCAT_MT_x_MGMT$fraction[3],
HF5_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -639,6 +684,7 @@ rbind.data.frame(
c(
HF5_IMP_MT_x_MGMT$fraction[7],
get("HF5_IMP-megahit_MT_x_MGMT")$fraction[7],
HF5_MT_x_naive$fraction[7],
HF5_MOCAT_MT_x_MGMT$fraction[7],
HF5_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -654,6 +700,8 @@ rbind.data.frame(
)
colnames(HF5.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
HF5.reads <- cbind(Dataset=rep("HF5", nrow(HF5.reads)), HF5.reads)
#####################################################################################################################################
### WW1 data summary
......@@ -666,6 +714,7 @@ rbind.data.frame(
c(
WW1_IMP_MG_x_MGMT$fraction[3],
get("WW1_IMP-megahit_MG_x_MGMT")$fraction[3],
WW1_MG_x_naive$fraction[3],
WW1_MOCAT_MG_x_MGMT$fraction[3],
WW1_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -682,6 +731,7 @@ rbind.data.frame(
c(
WW1_IMP_MG_x_MGMT$fraction[7],
get("WW1_IMP-megahit_MG_x_MGMT")$fraction[7],
WW1_MG_x_naive$fraction[7],
WW1_MOCAT_MG_x_MGMT$fraction[7],
WW1_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -698,6 +748,7 @@ rbind.data.frame(
c(
WW1_IMP_MT_x_MGMT$fraction[3],
get("WW1_IMP-megahit_MT_x_MGMT")$fraction[3],
WW1_MT_x_naive$fraction[3],
WW1_MOCAT_MT_x_MGMT$fraction[3],
WW1_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -714,6 +765,7 @@ rbind.data.frame(
c(
WW1_IMP_MT_x_MGMT$fraction[7],
get("WW1_IMP-megahit_MT_x_MGMT")$fraction[7],
WW1_MT_x_naive$fraction[7],
WW1_MOCAT_MT_x_MGMT$fraction[7],
WW1_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -729,6 +781,9 @@ rbind.data.frame(
)
colnames(WW1.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
WW1.reads <- cbind(Dataset=rep("WW1", nrow(WW1.reads)), WW1.reads)
#####################################################################################################################################
### WW2 data summary
......@@ -741,6 +796,7 @@ rbind.data.frame(
c(
WW2_IMP_MG_x_MGMT$fraction[3],
get("WW2_IMP-megahit_MG_x_MGMT")$fraction[3],
WW2_MG_x_naive$fraction[3],
WW2_MOCAT_MG_x_MGMT$fraction[3],
WW2_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -757,6 +813,7 @@ rbind.data.frame(
c(
WW2_IMP_MG_x_MGMT$fraction[7],
get("WW2_IMP-megahit_MG_x_MGMT")$fraction[7],
WW2_MG_x_naive$fraction[7],
WW2_MOCAT_MG_x_MGMT$fraction[7],
WW2_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -773,6 +830,7 @@ rbind.data.frame(
c(
WW2_IMP_MT_x_MGMT$fraction[3],
get("WW2_IMP-megahit_MT_x_MGMT")$fraction[3],
WW2_MT_x_naive$fraction[3],
WW2_MOCAT_MT_x_MGMT$fraction[3],
WW2_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -789,6 +847,7 @@ rbind.data.frame(
c(
WW2_IMP_MT_x_MGMT$fraction[7],
get("WW2_IMP-megahit_MT_x_MGMT")$fraction[7],
WW2_MT_x_naive$fraction[7],
WW2_MOCAT_MT_x_MGMT$fraction[7],
WW2_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -804,6 +863,7 @@ rbind.data.frame(
)
colnames(WW2.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
WW2.reads <- cbind(Dataset=rep("WW2", nrow(WW2.reads)), WW2.reads)
#####################################################################################################################################
### WW3 data summary
......@@ -816,6 +876,7 @@ rbind.data.frame(
c(
WW3_IMP_MG_x_MGMT$fraction[3],
get("WW3_IMP-megahit_MG_x_MGMT")$fraction[3],
WW3_MG_x_naive$fraction[3],
WW3_MOCAT_MG_x_MGMT$fraction[3],
WW3_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -832,6 +893,7 @@ rbind.data.frame(
c(
WW3_IMP_MG_x_MGMT$fraction[7],
get("WW3_IMP-megahit_MG_x_MGMT")$fraction[7],
WW3_MG_x_naive$fraction[7],
WW3_MOCAT_MG_x_MGMT$fraction[7],
WW3_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -848,6 +910,7 @@ rbind.data.frame(
c(
WW3_IMP_MT_x_MGMT$fraction[3],
get("WW3_IMP-megahit_MT_x_MGMT")$fraction[3],
WW3_MT_x_naive$fraction[3],
WW3_MOCAT_MT_x_MGMT$fraction[3],
WW3_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -864,6 +927,7 @@ rbind.data.frame(
c(
WW3_IMP_MT_x_MGMT$fraction[7],
get("WW3_IMP-megahit_MT_x_MGMT")$fraction[7],
WW3_MT_x_naive$fraction[7],
WW3_MOCAT_MT_x_MGMT$fraction[7],
WW3_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -879,6 +943,7 @@ rbind.data.frame(
)
colnames(WW3.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
WW3.reads <- cbind(Dataset=rep("WW3", nrow(WW3.reads)), WW3.reads)
#####################################################################################################################################
### WW4 data summary
......@@ -891,6 +956,7 @@ rbind.data.frame(
c(
WW4_IMP_MG_x_MGMT$fraction[3],
get("WW4_IMP-megahit_MG_x_MGMT")$fraction[3],
WW4_MG_x_naive$fraction[3],
WW4_MOCAT_MG_x_MGMT$fraction[3],
WW4_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -907,6 +973,7 @@ rbind.data.frame(
c(
WW4_IMP_MG_x_MGMT$fraction[7],
get("WW4_IMP-megahit_MG_x_MGMT")$fraction[7],
WW4_MG_x_naive$fraction[7],
WW4_MOCAT_MG_x_MGMT$fraction[7],
WW4_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -923,6 +990,7 @@ rbind.data.frame(
c(
WW4_IMP_MT_x_MGMT$fraction[3],
get("WW4_IMP-megahit_MT_x_MGMT")$fraction[3],
WW4_MT_x_naive$fraction[3],
WW4_MOCAT_MT_x_MGMT$fraction[3],
WW4_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -939,6 +1007,7 @@ rbind.data.frame(
c(
WW4_IMP_MT_x_MGMT$fraction[7],
get("WW4_IMP-megahit_MT_x_MGMT")$fraction[7],
WW4_MT_x_naive$fraction[7],
WW4_MOCAT_MT_x_MGMT$fraction[7],
WW4_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -954,6 +1023,7 @@ rbind.data.frame(
)
colnames(WW4.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
WW4.reads <- cbind(Dataset=rep("WW4", nrow(WW4.reads)), WW4.reads)
#####################################################################################################################################
### BG data summary
......@@ -966,6 +1036,7 @@ rbind.data.frame(
c(
BG_IMP_MG_x_MGMT$fraction[3],
get("BG_IMP-megahit_MG_x_MGMT")$fraction[3],
BG_MG_x_naive$fraction[3],
BG_MOCAT_MG_x_MGMT$fraction[3],
BG_metAmos_MG_x_MGMT$fraction[3],
# MG assm
......@@ -982,6 +1053,7 @@ rbind.data.frame(
c(
BG_IMP_MG_x_MGMT$fraction[7],
get("BG_IMP-megahit_MG_x_MGMT")$fraction[7],
BG_MG_x_naive$fraction[7],
BG_MOCAT_MG_x_MGMT$fraction[7],
BG_metAmos_MG_x_MGMT$fraction[7],
# MG assm
......@@ -998,6 +1070,7 @@ rbind.data.frame(
c(
BG_IMP_MT_x_MGMT$fraction[3],
get("BG_IMP-megahit_MT_x_MGMT")$fraction[3],
BG_MT_x_naive$fraction[3],
BG_MOCAT_MT_x_MGMT$fraction[3],
BG_metAmos_MT_x_MGMT$fraction[3],
# MG assm
......@@ -1014,6 +1087,7 @@ rbind.data.frame(
c(
BG_IMP_MT_x_MGMT$fraction[7],
get("BG_IMP-megahit_MT_x_MGMT")$fraction[7],
BG_MT_x_naive$fraction[7],
BG_MOCAT_MT_x_MGMT$fraction[7],
BG_metAmos_MT_x_MGMT$fraction[7],
# MG assm
......@@ -1029,7 +1103,33 @@ rbind.data.frame(
)
colnames(BG.reads) <- c("Assembly", "MG_mapped","MG_properly_paired","MT_mapped","MT_properly_paired")
BG.reads <- cbind(Dataset=rep("BG", nrow(BG.reads)), BG.reads)
### Bind all the tables
all.dat <- SM.reads
samples <- c("HF1", "HF2", "HF3", "HF4", "HF5", "WW1", "WW2", "WW3", "WW4", "BG")
for(i in seq_along(samples)){
print(samples[i])
dat.now <- get(paste(samples[i], "reads", sep="."))
all.dat <- rbind.data.frame(all.dat, dat.now)
}
prod.dat <- read.table("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/prodigal_analysis/prodigal_summary.tsv", header=T)
prod.dat$Assembly <- gsub("MetAMOS_MG", "MetAmos_MG", prod.dat$Assembly)
prod.dat$Assembly <- gsub("MetAMOS_MGMT", "MetAmos_MGMT", prod.dat$Assembly)
prod.dat$Assembly <- gsub("MetAMOS_MT", "MetAmos_MT", prod.dat$Assembly)
all.dat.1 <- merge(all.dat,prod.dat, by=c("Dataset", "Assembly"), all=T)
write.table(all.dat.1, "/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/comparison/data_usage/usage_gene_table.csv", row.names=F, quote=F, sep=",")
## Save image
#save.image("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/comparison/data_usage/data_usage.Rdat")
load("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/comparison/data_usage/data_usage.Rdat")
#load("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/comparison/data_usage/data_usage.Rdat")
#save.image("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/comparison/data_usage/data_usage-v2.Rdat")
#load("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/comparison/data_usage/data_usage-v2.Rdat")
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