consmat: Construct a consensus matrix from pileup.

In gschofl/DR2S: Dual redundant reference sequencing

Description

Accessor and replacement methods are available: n(consmat), ins(consmat), offsetBases(consmat), is.freq(consmat).

Usage

consmat(x, freq = TRUE, ...)

consmat(x) <- value

n(consmat)

n(consmat) <- value

ins(consmat)

ins(consmat) <- value

offsetBases(consmat)

offsetBases(consmat) <- value

is.freq(consmat)

Arguments

x	A pileup object. Additional inputs can be a matrix, tbl_df or consmat objects.
freq	If TRUE then frequencies are reported, otherwise counts.
...	Additional arguments such as n, offsetBases, insertions
value	The value to replace with.
consmat	The consmat object that is changed.

Details

consmat: a matrix with positions row names and nucleotides as column manes. A consmat object includes the attributes:

n

<integer>; Number of reads per row.

freq

<logical>; Is it a frequency matrix or a count matrix.

offsetBases

<integer>; OffsetBases

insertions

<integer>; Insertions

Value

A consmat object.

Examples

print("TODO: ADD EXAMPLES")
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gschofl/DR2S documentation built on May 17, 2019, 8:40 a.m.