# Protein Micro Array Data Management and Interactive Visualization

## Documentation for package ‘protGear’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

array_vars | List the array structure variables
best_CV_estimation | best CV estimation
bg_correct | bg_correct
buffer_spots | Extract buffer spots of data
check_sampleID_files | \\_End_Function_\\ # Check existing sample ID names
create_dir | Title Create directory function
cv_by_sample_estimation | cv by sample
cv_estimation | cv_estimation
extract_bg | extract bg
launch_protGear_interactive | launch_protGear_interactive
launch_select | launch_select
matrix_normalise | Normalize Arrays
merge_sampleID | Merge sample ID with the array data
minpositive | Get the minimum positive value
name_of_files | Object names of a list
output_trend_stats | Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests
plot_bg | Plot background
plot_buffer | Plot the buffer values
plot_FB | plot_FB
plot_normalised | Comparison of normalised data by sample
plot_normalised_antigen | Comparison of normalised data by feature
read_array_files | Read array files
read_array_visualize | Read a gpr file to visualize
rlm_normalise_matrix | Nomrmalise using RLM
tag_subtract | tag_subtract
visualize_slide | Visualize the slide mimicking the original scan image.
visualize_slide_2d | Visualize the slide mimicking the original scan image using a 2d plot.