rbamtools (version 2.16.17)

rangeSegCount-class: Class "rangeSegCount": Represents alignment counts in segments of genetic regions.

Description

rangeSegCount.

Objects from the Class

Objects can be created by calls of the form range<-rangeSegCount(object, coords, segments, complex).

Slots

position:

Integer. Vector of chromosomal positions which define the segments in which alignments are counted.

%

count:

Integer. Number of alignments which are located in the position segments

%

refname:

Character. Name of the reference sequence as given in the header section of the BAM file (e.g. 'chr1').

%

LN:

Integer. Total size of reference sequence (chromosome).

%

coords:

Numeric. A numeric vector giving the genomic coordinates from which alignments were counted.

%

complex:

Logical.

Methods

as.data.frame

signature(x="rangeSegCount"): Returns data.frame representation of aligns.

%

coerce

signature(from="rangeSegCount", to="data.frame"): Coercion of rangeSegCount to data.frame.

%

meltDownSegments

signature(object="rangeSegCount", factor="numeric"): Defines the factor by which the number of counting segments is shrinked. factor=2 means that counts for two adjacent segments are accumulated.

Details

Two kinds of coordinates are used: A) coords (numeric) containing seqid, start and end position (see also bamRange) which are used for reading alignments from a BAM file, and B) position (numeric) which contains an arbitrary sized vector. The position values define the borders of genomic segments in which alingments are counted. The segments usually would cover a whole chromosome and separates genetic and intergenic regions. The result is then the number of alignments in genetic and intergenetic regions which then can be used as gene expression estimates. The segments are defined as right open intervals. When the position is given by c(1,10,20) for example, the first segment is defined be nucleotide positions 1 to 9 and the second segment is 10 to 19. The counting mechanism only takes the alignment position into account. A possible overhang of the alingment over a segment boundary is not represented here (because this would complicate the model of 'counting' whole alignments.)

Examples

# NOT RUN {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# A) Open reader
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
idx<-paste(bam,"bai",sep=".")
# Open BAM file
reader<-bamReader(bam, idx=TRUE)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# B) Count range segment
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
coords <- c(0, 0, 2e4)
segments <- seq(14000, 20000, 20)
segcount<-rangeSegCount(reader, coords, segments)
segcount
dfr<-as.data.frame(segcount)
# }
# NOT RUN {
plot(count~position, dfr, type="l", las=1, bty="n", lwd=1.5)
# }