methylPipe (version 1.6.2)

BSprepare: Preparing tabular data to be used to feed a BSdata object

Description

Appending p-values and TABIX compressing tabular data containing DNA-methylation data so that they can be used to create a BSdata object.

Usage

BSprepare(files_location, output_folder, tabixPath, bc=1.5/100)

Arguments

files_location

character; the path to the files

output_folder

character; the path to the output files

tabixPath

character; the path to the Tabix application folder

bc

numeric; combined bisulfite conversion and sequencing error rate

Value

• Binomial p-values are added and a compressed file is created together with the Tabix index. P-values indicate for each Cytosine the probability of observing by chance the occurrence of unmethylated reads. The lower the p-value the higher the confidence in calling that Cytosine methylated.

Details

This function can be used to convert tabular files containing DNA-methylation base-resolution data so that they can be used to create a BSdata object. Genomic coordinates in the 1-base system are required, i.e. the first base of each chromosome should be at position 1. Files have to be tab-delimited and they have to contain the following columns: chromosome assignment (in the form chr1, .., chr22, chrX, chrY, chrM, chrC), genomic position (positive integer), strand (either - or +), methylation sequence context (either CG, CHG or CHH), number of sequencing reads with C calls (>0) at that genomic position, number of sequencing reads with T calls at that genomic position. Each file has to be sorted by genomic coordinate.

See Also

BSdata-class

Examples

#BSprepare("/path-to-input/","/path-to-output/", tabix="/path-to-tabix/tabix-0.2.6")