malaria: Malaria parasite genome variants

In tdhock/animint2: Animated Interactive Grammar of Graphics

Malaria parasite genome variants

Description

Two sequencing methods were used to measure genetic variants in malaria parasite yoelii yoelii, strain N67. High quality gold standard Sanger sequences were obtained for 45 amplicons, a small subset of the 14-chromosome genome. Next generation sequencing (NGS) was used to find genome-wide variants, but there is a lot more noise and so some false positive variants need to be filtered via thresholding the MQ score.

Usage

data("malaria")

Format

List of 8 data.frames: $ error.variants :'data.frame': 18800 obs. of 19 variables: $ regions :'data.frame': 14 obs. of 6 variables: $ amplicons :'data.frame': 45 obs. of 8 variables: $ chroms :'data.frame': 14 obs. of 2 variables: $ error.amplicons :'data.frame': 1800 obs. of 11 variables: $ filterVar.labels:'data.frame': 40 obs. of 3 variables: $ error.curves :'data.frame': 120 obs. of 4 variables: $ filterVar :'data.frame': 1 obs. of 2 variables:

Source

https://github.com/tdhock/malaria-evolution-viz

tdhock/animint2 documentation built on April 14, 2024, 4:22 p.m.