s1_normalize_raw_counts: s1 normalize raw counts function following Gale lab protocol
In galelab/GaleGEAnalysis: What the Package Does (One Line, Title Case)

Description Usage Arguments Examples

View source: R/s1_normalize_raw_counts_function.r

This function allows the normalization of raw counts following a general protocol developed by previous members of the gale lab

s1_normalize_raw_counts(
  countfile,
  targetfile,
  gene_conversion_file = FALSE,
  target_column = 10,
  batch_column = FALSE,
  blocking_column = FALSE,
  visualize_data = TRUE,
  filter_genes_below_counts = 0,
  filter_method = "sum",
  norm_method = "none",
  results_folder = "s1_norm_raw_counts_results",
  figres = 150
)

`countfile`	raw counts table (generally output by htseq).
`targetfile`	target file.
`target_column`	columns from the target file to build design matrix for future DE analysis
`blocking_column`	column to account sampling from the same animal multiple times
`filter_genes_below_counts`	filter out genes with counts below a certain value, (default set to 0).
`filter_method`	method by which to filter genes (sum or mean, sum is defualt)
`norm_method`	normalization method to use when normalizing LogCPM
`results_folder`	folder to store results in defualt is s1_norm_raw_counts_results
`figres`	resolution at which to output figures (default is 300).
`vizualize_data`	whether or not to generate figures (default set to true).

normalize_raw_counts(countfile="./p1_modified_count_matrix_results/count_file.txt", targetfile="./p1_modified_count_matrix_results/target_file.csv", gene_conversion_file="rhesus2human.csv", target_column=10, blocking_column=2, vizualize_data=TRUE, filter_genes_below_counts=0, figres=100)