MPU.callBases: MPILEUP Base Call Utility Functions

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

MPILEUP Base Call Utility Functions

Description

A collection of low level functions that manipulate the cryptic base call information extracted from BAM files by the SAMTOOLS MPILEUP utility. Most are intended to convert the cryptic notation into more R friendly formats.

Usage

MPU.callBases(baseCalls, referenceBase, minDepth = 3, mode = c("counts", "percents"))
MPU.strandDepth(baseCalls, pos = NULL)
MPU.callStringToTable(callStrings)
MPU.callTableToString(callTables)
MPU.callStringsToMatrix(callStrings)
MPU.callMatrixToBaseCounts(m, referenceBase, indelsToo = FALSE, normalize = FALSE)

Arguments

baseCalls	Vector of character strings from MPILEUP, that are in the cryptic ",,,..A,,..A,...,," format. One string for each nucleotide location.
referenceBase	Vector of single character bases, same length as baseCalls, that are the expected reference genome calls for those nucleotide locations.
minDepth	Integer minimum depth of base calls needed to make an Indel consensus. Only applies to locations that report at least one insertion or deletion. Indel nucleotides with too few base calls will disregard those calls and return the reference base.
mode	Returns the base distribution as either integer counts, or numeric percentages that sum to 100%
pos	Option vector of locations to use as the rownames for the resulting data frame.
callStrings	Character vector of base call strings in the compact "A=25;C=1;T=1" format.
callTables	A table or list of tables, where each table is a vector of named integer counts, and the names are the base calls.
m	A matrix of integer base call counts, as returned by MPU.callStringsToMatrix.

Details

Note that most all MPILEUP base call representations use the comma "," as a generic marker for "matches the genomic base", and only uses the typical A/C/G/T characters to denote SNPs, alternate base calls that do not match the expected genomic base.

Value

Function MPU.callBases returns a list:

calls	a vector of consensus base calls. Note that when the consensus is an Indel, that element may have zero or more than one character.
depth.table	a list of tables, where each element is the full distribution of observed base calls at that nucleotide location

Function MPU.strandDepth returns a data frame with 2 columns of integers, FWD_DEPTH, REV_DEPTH, giving the read depth for each strand separately.

Function MPU.callStringToTable returns a list of base call tables.

Function MPU.callTableToSring returns a character vector of base call strings.

Function MPU.callStringsToMatrix returns a matrix of base call depths, with columns for each possible base call , A C G T N Indel, and a row for each nucleotide position.

Function MPU.callMatrixToBaseCounts returns a matrix of final base call depths, after merging reference base information with the MPILEUP calls. The special comma "," notation is removed, the column names are the typical base calls A C G T Indel, and a row for each nucleotide position. The matrix values may be either integer counts, or normalized numeric values that sum each row to 100%

Author(s)

Bob Morrison

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.