Locations of DMLs and MACAU loci

Load libraries

list.of.packages <- c("tidyverse") #add new libraries here 
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

# Load all libraries 
lapply(list.of.packages, FUN = function(X) {
  do.call("require", list(X)) 
})
sessionInfo()

Where are differentially methylated loci located?

DML <- read_delim(here::here("analyses","20191120-DML-annotated.txt"), delim = '\t', 
                        col_names = c("contig.dml", "start.dml", "end.dml", "score.dml", "unknown", "contig.feat", "source", "feature", "start.feat", "end.feat", "score.feat", "strand", "frame", "attribute")) %>% as_tibble() %>% 
  mutate(ID=str_extract(attribute, "ID=(.*?);"), 
         Parent=str_extract(attribute, "Parent=(.*?);"),
         Name=str_extract(attribute, "Name=(.*?);"),
         Alias=str_extract(attribute, "Alias=(.*?);"),
         AED=str_extract(attribute, "AED=(.*?);"),
         eAED=str_extract(attribute, "eAED=(.*?);"),
         Note=str_extract(attribute, "Note=(.*?);"),
         Ontology_term=str_extract(attribute, "Ontology_term=(.*?);"),
         Dbxref=str_extract(attribute, "Dbxref=(.*?);"),
         ) %>%
  mutate_at("feature", as.factor)

## Parsed with column specification:
## cols(
##   contig.dml = col_character(),
##   start.dml = col_double(),
##   end.dml = col_double(),
##   score.dml = col_double(),
##   unknown = col_double(),
##   contig.feat = col_character(),
##   source = col_character(),
##   feature = col_character(),
##   start.feat = col_double(),
##   end.feat = col_double(),
##   score.feat = col_character(),
##   strand = col_character(),
##   frame = col_character(),
##   attribute = col_character()
## )

## Warning: 3 parsing failures.
## row col   expected    actual                                                                                         file
##   9  -- 14 columns 8 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/20191120-DML-annotated.txt'
##  10  -- 14 columns 8 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/20191120-DML-annotated.txt'
##  13  -- 14 columns 8 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/20191120-DML-annotated.txt'

par(mar=c(2,4,4,2))
barplot(table(DML$feature)[c("CDS", "exon", "gene", "mRNA", "3'UTR")], 
        main="Locations of DMLs between Hood Canal and South Sound Olys\n(10x cov. in any smpl)", 
        ylab="No. of loci", cex.main=1, cex.axis = .8)

Where are loci located where methylation is associated with oyster shell length?

Loci with 10x coverage across all samples

macau.all <- read_delim(here::here("analyses","macau","20191120-MACAU-10xall-features.txt"), delim = '\t', 
                        col_names = c("contig.locus", "start.locus", "end.locus", "unknown.column", "contig.feat", "source", "feature", "start.feat", "end.feat", "score", "strand", "frame", "attribute")) %>% as_tibble() %>%
  mutate(ID=str_extract(attribute, "ID=(.*?);"), 
         Parent=str_extract(attribute, "Parent=(.*?);"),
         Name=str_extract(attribute, "Name=(.*?);"),
         Alias=str_extract(attribute, "Alias=(.*?);"),
         AED=str_extract(attribute, "AED=(.*?);"),
         eAED=str_extract(attribute, "eAED=(.*?);"),
         Note=str_extract(attribute, "Note=(.*?);"),
         Ontology_term=str_extract(attribute, "Ontology_term=(.*?);"),
         Dbxref=str_extract(attribute, "Dbxref=(.*?);")) %>%
  mutate_at("feature", as.factor)

## Parsed with column specification:
## cols(
##   contig.locus = col_character(),
##   start.locus = col_double(),
##   end.locus = col_double(),
##   unknown.column = col_double(),
##   contig.feat = col_character(),
##   source = col_character(),
##   feature = col_character(),
##   start.feat = col_double(),
##   end.feat = col_double(),
##   score = col_character(),
##   strand = col_character(),
##   frame = col_character(),
##   attribute = col_character()
## )

## Warning: 1 parsing failure.
## row col   expected    actual                                                                                                       file
##  36  -- 13 columns 7 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/macau/20191120-MACAU-10xall-features.txt'

par(mar=c(2,2,4,2))
barplot(table(macau.all$feature)[c("CDS", "exon", "gene", "mRNA", "3'UTR")], 
        main="Locations of MACAU-identified loci (10x cov. in all smpl)", 
        ylab="No. of loci", cex.main=1, cex.axis = 1)

Where are loci located where methylation is associated with oyster shell length?

Loci with 10x coverage across any sample

macau.any <- read_delim(here::here("analyses","macau","20191120-MACAU-10xany-features.txt"), delim = '\t', 
                        col_names = c("contig.locus", "start.locus", "end.locus", "unknown.column", "contig.feat", "source", "feature", "start.feat", "end.feat", "score", "strand", "frame", "attribute")) %>% as_tibble() %>%
  mutate(ID=str_extract(attribute, "ID=(.*?);"), 
         Parent=str_extract(attribute, "Parent=(.*?);"),
         Name=str_extract(attribute, "Name=(.*?);"),
         Alias=str_extract(attribute, "Alias=(.*?);"),
         AED=str_extract(attribute, "AED=(.*?);"),
         eAED=str_extract(attribute, "eAED=(.*?);"),
         Note=str_extract(attribute, "Note=(.*?);"),
         Ontology_term=str_extract(attribute, "Ontology_term=(.*?);"),
         Dbxref=str_extract(attribute, "Dbxref=(.*?);"),
         ) %>%
  mutate_at("feature", as.factor)

## Parsed with column specification:
## cols(
##   contig.locus = col_character(),
##   start.locus = col_double(),
##   end.locus = col_double(),
##   unknown.column = col_double(),
##   contig.feat = col_character(),
##   source = col_character(),
##   feature = col_character(),
##   start.feat = col_double(),
##   end.feat = col_double(),
##   score = col_character(),
##   strand = col_character(),
##   frame = col_character(),
##   attribute = col_character()
## )

## Warning: 15 parsing failures.
## row col   expected    actual                                                                                                       file
##   5  -- 13 columns 7 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/macau/20191120-MACAU-10xany-features.txt'
##  32  -- 13 columns 7 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/macau/20191120-MACAU-10xany-features.txt'
##  58  -- 13 columns 7 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/macau/20191120-MACAU-10xany-features.txt'
##  69  -- 13 columns 7 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/macau/20191120-MACAU-10xany-features.txt'
## 105  -- 13 columns 7 columns '/Users/laura/Documents/roberts-lab/paper-oly-mbdbs-gen/analyses/macau/20191120-MACAU-10xany-features.txt'
## ... ... .......... ......... ..........................................................................................................
## See problems(...) for more details.

par(mar=c(2,2,4,2))
barplot(table(macau.any$feature)[c("CDS", "exon", "gene", "mRNA", "3'UTR")], 
        main="Locations of MACAU-identified loci (10x cov. in any smpl)", 
        ylab="No. of loci", cex.main=1, cex.axis = 1)

Locations of DMLs and MACAU loci

Laura H Spencer

11/20/2019

Load libraries

Where are differentially methylated loci located?

Where are loci located where methylation is associated with oyster shell length?

Loci with 10x coverage across all samples

Where are loci located where methylation is associated with oyster shell length?

Loci with 10x coverage across any sample