R functions

R custom functions that are useful for different omics analyses.

If you use one of these functions, please, mention me and give a star to this repository.

TO DOs

Functions and packages to consider:

• dplyr::: add_count(), mutate_if(), summarise_if()
• tidyr::: replace_na(), drop_na(), pivot_longer(), pivot_wider(), ùnite(), join_all(), complete(), full_seq(), unnest_wider(), unnest_longer(), gather()
• forcats::: fct_reorder(), fct_relevel(), fct_rev()

Rfunctions.R

Script that loads all the functions by doing source of the other R scripts present in this repository.

It use the R package here (if you don't have it).

Paths may have to be changed depending on the current directory where here works.

count_reads_table.R

Functions to count reads/counts from FastQC reports, BAM files and featureCounts summary outputs.

pcaplot2.R

pcaplot2()

It is a modification of the function pcaplot from R package pcaExplorer that allows to change points shapes.

It takes rlog-transformed DEseq2 dataframe as input.

Packages used:

• ggplot2

pieAnno.R

It includes two functions:

filterAnno()

Takes the output of annotatePeak function from ChIPseeker package and changes the annotation features to "Promoter" and "Distal", or "Promoter", "Distal" and "Gene body".

pieAnno()

Takes the output of annotatePeak, calls filterAnno() and plots a ggplot2-based pie chart with only distal and promoter features.

Packages used:

• ggplot2

signals_in_regions.R

Functions that compute the coverage (BIGWIG) over several regions (BED).

• Input:
  • character vector with the path(s) to bed files;
  • character vector with the path(s) to bigwig files.