In caravagnalab/LineaGT: lineaGT

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE
)

library(lineaGT)
# library(magrittr)

The fit function of the library requires two input datasets: one dataset with the coverage observation and one with the mutations variant allele number of reads and per-locus depth.

Coverage Dataframe

The first dataframe requires the following columns:

• IS: the integration site ID,

• timepoints: the longitunal timepoint,

• lineage: the cell lineage name,

• coverage the number of reads assigned to the ISs.

If lineage and timepoints columns are not present, a single longitunal observation and single lineage will be assumed.

A dataset example is the following:

data(cov.df.example)
cov.df.example

Mutations Dataframe

The second dataframe requires the following columns:

• IS: the integration site ID,

• mutation: the mutation ID,

• timepoints: the longitunal timepoint,

• lineage: the cell lineage name,

• alt: the per-locus variant allele number of reads,

• dp: the per-locus total number of reads, hence the per-locus depth.

A dataframe example is the following:

data(vaf.df.example)
vaf.df.example

caravagnalab/LineaGT documentation built on June 13, 2025, 1:58 p.m.