Assessing Immune Factors in Maternal Milk and Paired Infant Plasma Antibody Binding to Human Rhinoviruses
The code provided here will process the peptide array data available under 10.5281/zenodo.8269759 and return plasma IgG epitope calls and breast milk IgA epitope calls which are the same as the epitope calls provided as supplemental data with our manuscript.
- Clone this repo.
- Download the input data (IgG.lseq.tsv and IgA.lseq.tsv) from Zenodo at https://zenodo.org/records/8269759 and add to this repo directory.
- Run
epitope_calls_analysis.R.
This code was tested with R-4.0.5 and R 4.1.0 and requires the
dplyr, Matrix, data.table, openxlsx, tidyr, and purrr packages and
their dependencies.
An example R-4.0.5 session info is provided below:
version R version 4.0.5 (2021-03-31)
os macOS 13.4.1
system x86_64, darwin17.0
Packages ───────────────────────────────────────────────────────────────────────
package version
circlize 0.4.15
cli 3.6.1
colorspace 2.0-3
data.table 1.14.4
dichromat 2.0-0.1
digest 0.6.29
dplyr 1.1.2
ellipsis 0.3.2
evaluate 0.17
fansi 1.0.3
fastmap 1.1.0
forcats 0.5.1
generics 0.1.3
GlobalOptions 0.1.2
glue 1.6.2
htmltools 0.5.5
httr 1.4.4
knitr 1.40
lattice 0.20-45
lifecycle 1.0.3
magrittr 2.0.3
mapproj 1.2.8
maps 3.4.0
Matrix 1.5-3
openxlsx 4.2.5.1
pals 1.7
pillar 1.9.0
pkgconfig 2.0.3
purrr 0.3.4
qs 0.25.3
R6 2.5.1
RApiSerialize 0.1.2
Rcpp 1.0.8
RcppParallel 5.1.5
rlang 1.1.1
rmarkdown 2.17
rstudioapi 0.14
sessioninfo 1.2.2
shape 1.4.6
stringfish 0.15.5
stringi 1.7.6
stringr 1.4.1
tibble 3.2.1
tidyr 1.2.0
tidyselect 1.2.0
utf8 1.2.2
vctrs 0.6.3
withr 2.5.0
xfun 0.39
yaml 2.3.5
zip 2.2.2