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
set.seed(123) # for reproducibility of the example
shmulateTree(sequence, graph)

            name                                      sequence distance
1      Inferred1 NGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATAGTTTA        0
2 GN5SHBT07JDYW5 NGATCTGACGACCCGGCCGTGTATTACTGTGCGAGAGATAGTTCA        2
3 GN5SHBT03EP4KC NCATCTGACGACCCGGCCGTAAATTACTGTGCGAGAGATAGTTCA        3
4 GN5SHBT01AKANC NGATCAGACGACACGGCCGTCTATTACTGTGCGAGATATACTTTA        4
5 GN5SHBT01A3SFZ NGATGTGACGACCCGTCTGTGTACTACTATGCGGGAGATAGTTCA        6
6 GN5SHBT08HUU7M NCATCTGACGACCCGGTCATAAATTACTGTGCGAGAGATAGTTTA        3
7 GN5SHBT04CEA6I NGATCTGACGACCCGGCCGTGTATTACTGTGCGACAGATAGTTCA        1
8 GN5SHBT06IXJIH NGATCTGACGACCCGGCCGTGTATTGCTGTGCGAGAGATAGTTCA        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
set.seed(321) # for reproducibility of the example
shmulateTree(sequence, graph, targetingModel=MK_RS5NF,
field="sample_id", exclude=NA, junctionWeight=0.2)

            name                                      sequence distance
1 GN5SHBT07JDYW5 NGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATAGTTTA        0
2 GN5SHBT03EP4KC NGATCTGACGACACGGCCGTGTTTTACTGTGGGAGAAATCGTTTA        4
3 GN5SHBT01A3SFZ NGATCTGACGACATGACCGTGTTTAATTGTGTGAGAGATAGTTTT        7
4 GN5SHBT08HUU7M NGATTTGACGACACGGCCGTATTTTACTGTGGGAAAAATCGTTTA        3
5 GN5SHBT04CEA6I NGATCTGACGACACGGCCGTGTATTACTGTGCGAAAGATAGTTTA        1
6 GN5SHBT06IXJIH NGATCTGACGACACGGCCGTGTATTCCTGTGCGAGAGATAGTTTA        1

See also¶

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