In roeder/mapstatHelpers: Helper Functions for the Mapstat Format and Friends

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mapstatHelpers

The mapstatHelpers package provides a few functions that will help you import sequencing results obtained with the new workflow at CGE, which involves file formats such as .mapstat and .refdata.

Installation

You need to install the package directly from GitHub using the install_github() function from the devtools package. Of course this means that you might need to install devtools first:

install.packages("devtools")
devtools::install_github("roeder/mapstatHelpers")

Mapstat metadata

Every .mapstat file starts with six lines containing information on the mapping that was performed in order to obtain the results within that file.

Here is an example header:

## method   KMA
## version  1.2.8
## database ResFinder_20190213
## fragmentCount    32955753
## date 2019-07-23
## command  /home/projects/cge/apps/kma/1.2.8/kma/kma -ipe "/home/projects/cge/analysis/EFFORT/trim/pig/1001-17-001_R1_001.trim.fq.gz" "/home/projects/cge/analysis/EFFORT/trim/pig/1001-17-001_R2_001.trim.fq.gz" -o "/home/projects/cge/analysis/EFFORT/kma_resfinder/2019-07-23_all_EFFORT_with_replicates_merged/ResFinder_20190213/ResFinder_20190213__1001-17-001_R1_001" -t_db /home/databases/metagenomics/kma_db/ResFinder/ResFinder_20190213 -mem_mode -ef -1t1 -cge -shm 1 -t 1 

The package offers functions for importing the mapping metadata of many .mapstat files at once. Use get_multiple_metadata() to load the metadata of all .mapstat files in a directory. The function returns a data frame and prints a summary of the metadata across all samples:

library(mapstatHelpers)
problem_example_dir <- "../kma_EFFORT/data/2019-07-23_all_EFFORT_with_replicates_merged/genomic_20190404/"
nice_example_dir <- "../kma_EFFORT/data/2019-07-23_all_EFFORT_with_replicates_merged/ResFinder_20190213/"

library(mapstatHelpers)
nice_example_dir <- "~/projects/nice_mapping/mapstat/"

nice_metadata <- get_multiple_metadata(nice_example_dir)

You can inspect the data frame containing the imported metadata. Note that the name of each file is added in the column sample_id:

head(nice_metadata)

An additional warning message is printed if multiple mapping methods, method versions or database versions are detected:

problem_example_dir <- "~/projects/problematic_mapping/mapstat/"

problem_metadata <- get_multiple_metadata(problem_example_dir)

After importing the metadata table, you can always print the summary again by using check_metadata():

check_metadata(problem_metadata)

Importing mapstat files

Once you are happy with the metadata corresponding to all your .mapstat files, you can go ahead and import the actual content, i.e. the mapping results, using read_multiple_mapstats():

nice_mapstat_results <- read_multiple_mapstats(nice_example_dir)
head(nice_mapstat_results)

Importing refdata files

Last (and kind of least), the package also allows the import of .refdata files. We use such files for the taxonomic annotation corresponding to our large genome databases. Import them with read_refdata():

genomic_refdata <- read_refdata("~/projects/nice_mapping/genomic_20190404.refdata")

roeder/mapstatHelpers documentation built on Nov. 5, 2019, 3:14 a.m.