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How to edit mapping file and merge with existing phyloseq object?
I am working in phyloseq and am having trouble editing my mapping data once I have already created a phyloseq object. I think the problem is with how I'm trying to merge the edited data with the object, but I can't pinpoint the exact problem.
Everything with initially setting up the phyloseq object is fine and looks like this:
#Sequence chimera checked from dada2
seqtab <- readRDS("seqtab.rds")
#Taxonomic assignments
taxa <- read.csv("taxonomy.csv",sep=",",row.names=1)
taxa <- as.matrix(taxa)
#Mapping file
mapfile <- "map.txt"
map <- import_qiime_sample_data(mapfile)
head(map)
#Creating phyloseq object.
ps <- phyloseq(otu_table(seqtab, taxa_are_rows=FALSE),
sample_data(map),
tax_table(taxa))
However, once I have this set up I want to be able to make edits to the mapping data, preferably using dplyr, and then merge it back with the phyloseq object. This is how I've been trying to do it:
#Edit columns in dplyr
split <- data.frame(sample_data(ps))
split <- split %>%
separate(Date, c("Day", "Month", "Year"), sep = "-")
#Merge sample dataframes
sam <- data.frame(sample_data(ps))
split <- merge(split, sam, by = "SampleID")
When I do this and just look at my sample data, the columns have been split correctly. However, when I look at the phyloseq object, the columns have not been split properly. Does anyone have suggestions for where I'm going wrong?
merge dplyr phyloseq
asked Nov 19 '18 at 15:47
IOS917
62
add a comment |
I am working in phyloseq and am having trouble editing my mapping data once I have already created a phyloseq object. I think the problem is with how I'm trying to merge the edited data with the object, but I can't pinpoint the exact problem.
Everything with initially setting up the phyloseq object is fine and looks like this:
#Sequence chimera checked from dada2
seqtab <- readRDS("seqtab.rds")
#Taxonomic assignments
taxa <- read.csv("taxonomy.csv",sep=",",row.names=1)
taxa <- as.matrix(taxa)
#Mapping file
mapfile <- "map.txt"
map <- import_qiime_sample_data(mapfile)
head(map)
#Creating phyloseq object.
ps <- phyloseq(otu_table(seqtab, taxa_are_rows=FALSE),
sample_data(map),
tax_table(taxa))
However, once I have this set up I want to be able to make edits to the mapping data, preferably using dplyr, and then merge it back with the phyloseq object. This is how I've been trying to do it:
#Edit columns in dplyr
split <- data.frame(sample_data(ps))
split <- split %>%
separate(Date, c("Day", "Month", "Year"), sep = "-")
#Merge sample dataframes
sam <- data.frame(sample_data(ps))
split <- merge(split, sam, by = "SampleID")
When I do this and just look at my sample data, the columns have been split correctly. However, when I look at the phyloseq object, the columns have not been split properly. Does anyone have suggestions for where I'm going wrong?
merge dplyr phyloseq
asked Nov 19 '18 at 15:47
IOS917
62
add a comment |
I am working in phyloseq and am having trouble editing my mapping data once I have already created a phyloseq object. I think the problem is with how I'm trying to merge the edited data with the object, but I can't pinpoint the exact problem.
Everything with initially setting up the phyloseq object is fine and looks like this:
#Sequence chimera checked from dada2
seqtab <- readRDS("seqtab.rds")
#Taxonomic assignments
taxa <- read.csv("taxonomy.csv",sep=",",row.names=1)
taxa <- as.matrix(taxa)
#Mapping file
mapfile <- "map.txt"
map <- import_qiime_sample_data(mapfile)
head(map)
#Creating phyloseq object.
ps <- phyloseq(otu_table(seqtab, taxa_are_rows=FALSE),
sample_data(map),
tax_table(taxa))
However, once I have this set up I want to be able to make edits to the mapping data, preferably using dplyr, and then merge it back with the phyloseq object. This is how I've been trying to do it:
#Edit columns in dplyr
split <- data.frame(sample_data(ps))
split <- split %>%
separate(Date, c("Day", "Month", "Year"), sep = "-")
#Merge sample dataframes
sam <- data.frame(sample_data(ps))
split <- merge(split, sam, by = "SampleID")
When I do this and just look at my sample data, the columns have been split correctly. However, when I look at the phyloseq object, the columns have not been split properly. Does anyone have suggestions for where I'm going wrong?
merge dplyr phyloseq
asked Nov 19 '18 at 15:47
IOS917
62
I am working in phyloseq and am having trouble editing my mapping data once I have already created a phyloseq object. I think the problem is with how I'm trying to merge the edited data with the object, but I can't pinpoint the exact problem.
Everything with initially setting up the phyloseq object is fine and looks like this:
#Sequence chimera checked from dada2
seqtab <- readRDS("seqtab.rds")
#Taxonomic assignments
taxa <- read.csv("taxonomy.csv",sep=",",row.names=1)
taxa <- as.matrix(taxa)
#Mapping file
mapfile <- "map.txt"
map <- import_qiime_sample_data(mapfile)
head(map)
#Creating phyloseq object.
ps <- phyloseq(otu_table(seqtab, taxa_are_rows=FALSE),
sample_data(map),
tax_table(taxa))
However, once I have this set up I want to be able to make edits to the mapping data, preferably using dplyr, and then merge it back with the phyloseq object. This is how I've been trying to do it:
#Edit columns in dplyr
split <- data.frame(sample_data(ps))
split <- split %>%
separate(Date, c("Day", "Month", "Year"), sep = "-")
#Merge sample dataframes
sam <- data.frame(sample_data(ps))
split <- merge(split, sam, by = "SampleID")
When I do this and just look at my sample data, the columns have been split correctly. However, when I look at the phyloseq object, the columns have not been split properly. Does anyone have suggestions for where I'm going wrong?
merge dplyr phyloseq
merge dplyr phyloseq
asked Nov 19 '18 at 15:47
IOS917
62
asked Nov 19 '18 at 15:47
IOS917
62
asked Nov 19 '18 at 15:47
IOS917
62
asked Nov 19 '18 at 15:47
IOS917
62
asked Nov 19 '18 at 15:47
IOS917
62
62
add a comment |
add a comment |
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