calculate_polya_stats: Calculates basic statistics for polya lengths

In smaegol/nanotail: Analysis and visualisation of Nanopolish-based polyA lengths estimations

Calculates basic statistics for polya lengths

Description

Takes polyA predictions table as input and checks if there is significant difference in polyA lengths between chosen conditions for each transcript. By default, Wilcoxon Rank Sum (wilcox.test) test is used.

Usage

calculate_polya_stats(
  polya_data,
  transcript_id_column = "transcript",
  min_reads = 0,
  grouping_factor = "sample_name",
  condition1 = NA,
  condition2 = NA,
  stat_test = "Wilcoxon",
  alpha = 0.05,
  add_summary = TRUE,
  length_summary_to_show = "gm_mean",
  ...
)

Arguments

polya_data	input table with polyA predictions
transcript_id_column	name of the column with transcript ids (default = "transcript")
min_reads	minimum number of reads to include transcript in the analysis
grouping_factor	which column defines groups (default: sample_name)
condition1	if grouping_factor has more than 2 levels, which level use for comparison
condition2	if grouping_factor has more than 2 levels, which level use for comparison
stat_test	what statistical test to use for testing, currently supports "Wilcoxon" (for wilcox.test), "KS" (for ksTest from FSA package) or "glm" (for glm)
alpha	alpha value to consider a hit significant (default - 0.05)
add_summary	add summary (mean polya lengths, counts) to statistics results?
length_summary_to_show	which length summary to show ("median"/"mean"/"gm_mean")
...	additional parameters to pass to .polya_stats (custom_glm_formula,use_dwell_time)

Value

summary table with pvalues and median/mean values associated to each transcript

smaegol/nanotail documentation built on June 29, 2024, 12:35 a.m.