shmulateTree - Simulate mutations in a lineage tree

Description

shmulateTree returns a set of simulated sequences generated from an input sequence and a lineage tree. The input sequence is used to replace the most recent common ancestor (MRCA) node of the igraph object defining the lineage tree. Sequences are then simulated with mutations corresponding to edge weights in the tree. Sequences will not be generated for groups of nodes that are specified to be excluded.

Usage

shmulateTree(
sequence,
graph,
targetingModel = HH_S5F,
field = NULL,
exclude = NULL,
junctionWeight = NULL,
start = 1,
end = nchar(sequence)
)

Arguments

sequence
string defining the MRCA sequence to seed mutations from.
graph
igraph object defining the seed lineage tree, with vertex annotations, whose edges are to be recreated.
targetingModel
5-mer TargetingModel object to be used for computing probabilities of mutations at each position. Defaults to HH_S5F.
field
annotation to use for both unweighted path length exclusion and consideration as the MRCA node. If NULL do not exclude any nodes.
exclude
vector of annotation values in field to exclude from potential MRCA set. If NULL do not exclude any nodes. Has no effect if field=NULL.
junctionWeight
fraction of the nucleotide sequence that is within the junction region. When specified this adds a proportional number of mutations to the immediate offspring nodes of the MRCA. Requires a value between 0 and 1. If NULL then edge weights are unmodified from the input graph.
start
Initial position in sequence where mutations can be introduced. Default: 1
end
Last position in sequence where mutations can be introduced. Default: last position (sequence length).

Value

A data.frame of simulated sequences with columns:

  • name: name of the corresponding node in the input graph.
  • sequence: mutated sequence.
  • distance: Hamming distance of the mutated sequence from the seed sequence.

Examples

# Load example lineage and define example MRCA
data(ExampleTrees, package="alakazam")
graph <- ExampleTrees[[17]]
sequence <- "NGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATAGTTTA"

# Simulate using the default human 5-mer targeting model
shmulateTree(sequence, graph)


            name                                      sequence distance
1      Inferred1 NGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATAGTTTA        0
2 GN5SHBT07JDYW5 NGATCTGCCGACACGGCCGTGCATTACTGTGCGAGAGATAGTTTA        2
3 GN5SHBT03EP4KC NGATCCGCCGACACGACCGTGCATTACTGTGCGAGAGATACTTTA        3
4 GN5SHBT01AKANC NGATCTGACGACACGGCCGTCTATTTCTGTGCGGGAGATCGTTTA        4
5 GN5SHBT01A3SFZ NGATCTGCCGACGCGGCTGTGCATGACTGTGCGGGAGAAAGTTTG        6
6 GN5SHBT08HUU7M NGATCCGCCGACACGACCGTGCATGACTGTGCGAGAAACACTTTA        3
7 GN5SHBT04CEA6I NGATCTGCCGACGCGGCCGTGCATTACTGTGCGAGAGATAGTTTA        1
8 GN5SHBT06IXJIH NGATCTGCCGACACGGCCGTGCAATACTGTGCGAGAGATAGTTTA        1



# Simulate using the mouse 5-mer targeting model
# Exclude nodes without a sample identifier
# Add 20% mutation rate to the immediate offsprings of the MRCA
shmulateTree(sequence, graph, targetingModel=MK_RS5NF,
field="sample_id", exclude=NA, junctionWeight=0.2)

            name                                      sequence distance
1 GN5SHBT07JDYW5 NGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATAGTTTA        0
2 GN5SHBT03EP4KC NTATATGACGACACGGCCGTGTATTACTGTGTGAGAGATACTTTA        4
3 GN5SHBT01A3SFZ NAATCTGACGACATGGCCATATATTACTGTGCGAGAGAAACTTTT        7
4 GN5SHBT08HUU7M NTATGTGACGACACGACCGTGTCTTACTGTGTGAGAGATACTTTA        3
5 GN5SHBT04CEA6I NGATCTGACGACACGACCGTGTATTACTGTGCGAGAGATAGTTTA        1
6 GN5SHBT06IXJIH NGATCTGACGACACGGCCGTATATTACTGTGCGAGAGATAGTTTA        1

See also

See shmulateSeq for imposing mutations on a single sequence. See HH_S5F and MK_RS5NF for predefined TargetingModel objects.