While originally designed for B cells, Dowser also supports phylogenetic inference for non B cells, especially cells evolving from a known ancestral sequence, such as tumor lineages.
If sequences are from a single lineage, the only requirement for
non-B cell data is that the sequences supplied to
formatClones are aligned and in a data.frame with a column
for sequences and a column for sequence IDs. If from multiple lineages,
they can be deliminated using the clone_id column.
In the code block below, we show how trees can be built using data with only sequence IDs, sequences, and germline sequences.
library(dowser)
data(ExampleAirr)
ExampleAirr <- dplyr::select(dplyr::filter(ExampleAirr, clone_id=="3128"),
sequence_id, sequence_alignment, germline_alignment)
clones <- formatClones(ExampleAirr, germ="germline_alignment")## [1] "v_call, j_call, and junc_len not found in data. Using non B cell mode\n. Setting use_regions to FALSE."Note that if specified v_call, j_call, and
junction_length columns are not found in the input
data.frame, the options use_regions will be set to false,
as it is only for BCR sequences. If not already present, the
clone_id and locus columns will be added to
the dataframe with values 0 and “N”, respectively.
When using getTimeTrees or
getTimeTreesIterate, a meaninful germline is not required.
Instead, you can set a germline_alignment which is series
of N nucleotides the same length as the sequences in the
sequence_alignment column, and set
include_germline=FALSE.