SICtools (version 1.2.2)

snpDiff: main function to test point differences between the two bam files

Description

test base count (A,T,G,C) difference at a given position between the two bam files. The base count matrix is tested by fisher exact test and euclidean distance. If nothing difference, NULL will be returned.

Usage

snpDiff(bam1, bam2, refFsa, regChr, regStart, regEnd, minBaseQuality = 13, minMapQuality = 0, nCores = 1, pValueCutOff = 0.05, baseDistCutOff = 0.1,verbose = TRUE)

Arguments

bam1

the first bam file to be compared

bam2

the second bam file to be compared

refFsa

the reference fasta file used for bam1 and bam2 alignments

regChr

chromosome name of the region of interest, it should match the chromosome name in reference name

regStart

the start position (1-based) of the region of interest

regEnd

the end position (1-based) of the region of interest

minBaseQuality

the minimum base quality to be used for base count

minMapQuality

the minimum read mapping quality to be used for base count

nCores

number of thread used for calculate in parallel

pValueCutOff

p.value cutoff from fisher.test to display output. If there is no difference between two compared positions (p.value = 1 and d.value = 0), NULL will be returned even setting pValueCutOff = 1.

baseDistCutOff

euclidean distance cutoff from dist(,method='euclidean') to display output. If there is no difference between two compared positions (p.value = 1 and d.value = 0), NULL will be returned even setting baseDistCutOff = 0.

verbose

print progress on screen, default = TRUE.

Value

: returns a data.frame with difference information: chromosome, position, reference base, base count (A,C,G,T,N) for two bam files, p.value (fisher exact test of these base counts) and d.value (euclidean distance of these base counts)

References

Morgan M, Pages H, Obenchain V and Hayden N. Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import.

Examples

bam1 <- system.file(package='SICtools','extdata','example1.bam')
bam2 <- system.file(package='SICtools','extdata','example2.bam')
refFsa <- system.file(package='SICtools','extdata','example.ref.fasta')

snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,baseDistCutOff=0)