sort_rank_mean_expr: Create a rank-response data frame

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

Create a rank-response data frame

Description

Create a rank-response data frame

Usage

sort_rank_mean_expr(
  expression_df,
  expression_src,
  binding_df,
  binding_src,
  lfc_thres,
  padj_thres,
  rank_resolution = 5,
  num_rows = 30
)

Arguments

expression_df	a three column dataframe with the column names c('gene', 'log2FoldChange', 'padj') which describes expression data. It may have more columns, but those three must exist
expression_src	the source of the data, eg 'kemmeren' or 'brentlab'
binding_df	a two column dataframe dataframe with the columns c('gene', 'binding_signal'). It may have more columns, but those must exist
binding_src	the source of the data, eg 'chip-chip' or 'calling-cards'
lfc_thres	expression log2foldchange threshold. default is 0
padj_thres	expression padj threshold. default is .05
rank_resolution	how to bin ranks. Default is 10, which means that ranks are binned into groups of 10 (eg the first group are the 10 highest)
num_rows	the number of rows to return. Default is 15. For instance, if the rank_resolution is 10, and you only want to look at the first 150 ranked genes, then num_rows is 15.

Value

a rank_response dataframe

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.