adjustMethylC: Adjust measured 5mC levels using 5hmC levels

In methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

Measured 5mC levels via bisulfite sequencing might be a combination of 5hmC and 5mC levels since bisulfite sequencing can not distinguish between the two. This function can adjust 5mC levels of a bisulfite sequencing experiment if the user supplies corresponding 5hmC levels from the same sample.

Usage

adjustMethylC(mc,hmc,save.db,...,chunk.size)

## S4 method for signature 'methylRaw,methylRaw'
adjustMethylC(mc, hmc, save.db = FALSE, ..., chunk.size = 1e+06)

## S4 method for signature 'methylRawList,methylRawList'
adjustMethylC(mc, hmc, save.db = FALSE, ..., chunk.size = 1e+06)

## S4 method for signature 'methylRawDB,methylRawDB'
adjustMethylC(mc, hmc, save.db = TRUE, ..., chunk.size = 1e+06)

## S4 method for signature 'methylRawListDB,methylRawListDB'
adjustMethylC(mc, hmc, save.db = TRUE, ..., chunk.size = 1e+06)

Arguments

mc	a methylRawList, methylRaw, methylRawDB or methylRawListDB containing 5mC levels of a sample or set of samples
hmc	a methylRawList, methylRaw, methylRawDB or methylRawListDB containing 5hmC levels of a sample or set of samples. If a methylRawList or methylRawListDB given the sample order should be same as "mc" methylRawList or methylRawListDB object.
save.db	A Logical to decide whether the resulting object should be saved as flat file database or not, default: explained in Details sections
...	optional Arguments used when save.db is TRUE suffix A character string to append to the name of the output flat file database, only used if save.db is true, default actions: append “_filtered” to current filename if database already exists or generate new file with filename “sampleID_filtered” dbdir The directory where flat file database(s) should be stored, defaults to getwd(), working directory for newly stored databases and to same directory for already existing database dbtype The type of the flat file database, currently only option is "tabix" (only used for newly stored databases)
chunk.size	Number of rows to be taken as a chunk for processing the methylRawDB or methylRawListDB objects (default: 1e6)

Value

returns adjusted 5-methyl cytosine levels in the form of methylRawList, methylRaw, methylRawDB or methylRawListDB object depending on the input object

Details

The parameter chunk.size is only used when working with methylRawDB or methylRawListDB objects, as they are read in chunk by chunk to enable processing large-sized objects which are stored as flat file database. Per default the chunk.size is set to 1M rows, which should work for most systems. If you encounter memory problems or have a high amount of memory available feel free to adjust the chunk.size.

The parameter save.db is per default TRUE for methylDB objects as methylRawDB and methylRawListDB, while being per default FALSE for methylRaw and methylRawList. If you wish to save the result of an in-memory-calculation as flat file database or if the size of the database allows the calculation in-memory, then you might change the value of this parameter.

References

1. Booth, Branco, et al. (2012). Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution. Science, 934

2. Yu, Hon, et al. (2012). Base-resolution analysis of 5-hydroxymethylcytosine in the Mammalian genome. Cell, 149(6), 1368-80.

Examples

# read 5hmC and 5mC files
hmc.file=system.file("extdata", "test1.myCpG.txt", package = "methylKit")
mc.file =system.file("extdata", "test2.myCpG.txt", package = "methylKit")

my5hmC=methRead( hmc.file,sample.id="hmc",assembly="hg18")
my5mC =methRead( mc.file,sample.id="mc",assembly="hg18")

# adjusting the 5mC levels using 5hmC levels
adjusted.5mC=adjustMethylC(my5mC,my5hmC)

methylKit documentation built on Jan. 30, 2021, 2 a.m.