compare_gene: Find the consensus genes by comparing the frequency of gene...

In JH-Zhou/HandyCNV: HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

Description

Do comparison of genes between multiple annotated gene frequency lists. The default genelist file was generate by call_gene function. If the users customize the genelists, it requires at least two columns in each gene list, including fixed column names name2(Gene name) and Frequency(frequency of gene)

Usage

compare_gene(
  gene_freq_1,
  gene_freq_2,
  gene_freq_3 = NULL,
  gene_freq_4 = NULL,
  common_gene_threshold = 3,
  title_1 = "list_1",
  title_2 = "list_2",
  title_3 = "list_3",
  title_4 = "list_4",
  height_1 = 10,
  width_1 = 14,
  folder = "compre_gene",
  col_1 = "red",
  col_2 = "yellow",
  col_3 = "dodgerblue",
  col_4 = "pink2",
  color_label = FALSE
)

Arguments

gene_freq_1	first genelist, the default file was generated from call_gene function
gene_freq_2	second genelist, the default file was generated from call_gene function
gene_freq_3	third genelist, the default file was generated from call_gene function
gene_freq_4	fourth genelist, the default file was generated from call_gene function
common_gene_threshold	integer input.could calculate by multiplying The Number of Sample by 0.05 or 0.1, et al
title_1	set title(two and three lists) or label(four lists) in figure
title_2	set title(two and three lists) or label(four lists) in figure
title_3	set title(two and three lists) or label(four lists) in figure
title_4	set title(two and three lists) or label(four lists) in figure
height_1	customize the height to save figure
width_1	customize the width to save figure
folder	set the name of folder to save results
col_1	set color for common_high in two gene lists comparison plot or the color of High frequency gene in multiple comparison heatmap plot
col_2	set color for common_low in two gene lists comparison plot or the color of Low frequency gene in multiple comparison heatmap plot
col_3	set color for High_Freq_list_1 in two gene lists comparison plot
col_4	set color for High_Freq_list_2 in two gene lists comparison plot
color_label	if TRUE, the color of gene labels will marked in heatmap, the red labels are genes that passed common threshold

Value

Comparison summary results and plots.

JH-Zhou/HandyCNV documentation built on Dec. 18, 2021, 12:25 a.m.