BayClone2 (version 1.1)

export_N_n: export_N_n function

Description

This function takes a VCF file as input and generates two output files (names are specified by users) which contains the total number of reads and the number of reads that bear a mutated sequence, respectively, at a particular locus in a specific tissue sample.

Usage

export_N_n(vcf_in_file,N_tot_out_file,n_alt_out_file)

Arguments

vcf_in_file

the name of the input VCF file.

N_tot_out_file

the output file name for total reads count (character string)

n_alt_out_file

the output file name for mutant reads count (character string)

Value

• The function generates two output files. -N_tot_out_file: the output file that contains a (S x T) matrix, where S is the number of loci and T is the number of samples. Each element represents total number of reads at a locus in a specific tissue sample.

  -n_alt_out_file: the output file that contains a (S x T) matrix, where S is the number of loci and T is the number of samples. Each element represents number of mutated reads at a locus in a tissue sample.

Details

Input VCF filename is passed as the first argument. Second and third arguments are the name of the output files.

Second file contains total number of reads at loci in all samples.

Third file contains total number of mutant reads at loci in all samples.

NOTE: Each row in both the output files represents one particular loci for all the samples. The output files may be used as data, N and n, for the function, BayClone2.

References

J. Lee, P. Mueller, S. Sengupta, K. Gulukota, Y. Ji, Bayesian Inference for Tumor Subclones Accounting for Sequencing and Structural Variants (http://arxiv.org/abs/1409.7158) Sengupta S, Gulukota K, Lee J, Mueller, P, Y. Ji, BayClone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data. Conference paper accepted for PSB 2015 and oral presentation

See Also

BayClone2, fn_post_C, fn_posterior_point

Examples

### Illustrate the functionality of the function export_N_n with an example
# please put the appropriate file names to run this function.
#library("BayClone2")
##INPUT FILE: test_Data.VCF
##OUTPUT FILES: N_tot.txt and n_alt.txt
#export_N_n("test_Data.VCF","N_tot.txt","n_alt.txt")

##LOAD THE OUTPUT FILES -- THE OUTPUT FILES CAN BE USED AS DATA FOR BAYCLONE2.
#N <- read.table("N_tot.txt")
#n <- read.table("n_alt.txt")