HandyCNV v1.1.7

What's news

1. New feature haplo_visual() to visualize haplotype that generate from get_haplotype()
2. Unify format of some inputs and outputs

HandyCNV v1.1.6

Current release: HandyCNV v1.1.6 Release Date: 2021/09/01

What's news

1. Add autosomal boundary data for other species in 'cnvr_plot' function, which will be used to plot CNVR map. Now it support the hg38 and hg19 of human, UMD3.1 and ARS-UCD1.2 of cattle, Oar_v4.0 of sheep, Sscrofa11.1 of Pig, galGal6 of Chicken, EquCab3.0 of Horse and UMICH_Zoey_3.1 of Dog.
2. Add conditions to automatically control the number of X axis labels that present in the figure of The Number of CNVs Detected per Individual.
3. Update Github pages with Vignettes

HandyCNV v1.1.5

What's news

Minor modifications, such as unifying input file formats and correcting spelling errors.

HandyCNV v1.1.4

What's new

Major improvements:

1. Most functions now support reading variable object as input files;
2. Most functions now support returning the main output as object to R environment for the further operation;
3. New function 'get_samples' to extract samples ID by searching interested gene from CNV annotation list.

Minor changes:

1. The 'call_cnvr' funtion now support generating CNVRs from CNV list that contains Chromosomes without CNVs information;
2. Add links of Horse_quCab2.0 genome reference and sheep 'oviAri3' reference genome into 'get_refgene' function;
3. Setup a standard table to support present comparison plot with empty group in 'compare_cnvr' function;
4. Add '-' as separator between the two recoded haplotypes in 'get_haplotype' function.

HandyCNV v1.1.3

What's new

1. New function to plot SNP density from SNP genotyping map.

2. Revised CNVs status distribution plot in 'cnv_summary_plot' function, force to appear the boxplot and line on chromosome that has no CNVs.

HandyCNV v1.1.2

What's New

Corrected the version number.

HandyCNV v1.1.1

What's new

Modify the version number in the Description file.

1. Update call_cnvr.R …

1. It used to only load CNV list from the local directory through a 'Path', now supports to read data in working environment by checking the type of input file;
2. Support to return the CNVR list to working environment.

2. Update cnv_clean.R …

1. Support to return Clean CNV List to working environment.

3. Update cnv_visualising.R …

1. Support to load CNV List from working environment.

4. Update compare_cnvr.R …

1. Add new function to generate the Unique and Mutual CNVRs by uniting the overlapped CNVRs between two results. There are two purposes for this work, one is to better understand the overlapping CNVRs, the other is to mark the common regions on CNVR distribution map;

5. Update 'cnvr_plot' …

1. Add 'overlap_cnvr' argument to support to mark overlapped region on CNVR distribution map;
2. Add 'label_prop' argument to show the proportion of CNVRs length to total length of relative chromosome on CNVR map;
3. Add 'chr_col' argument to customize the color of Chromosome;
4. Add 'overlap_col' argument to customize color of overlapped CNVRs
5. Reduce the margin of final CNVR distribution map.

6. Update compare_gene.R …

1. Add 'color_label' argument to display the color of genes that passed common threshold in the Heatmap;

HandyCNV v1.1.0

What's new

1. Update call_cnvr.R …

1. It used to only load CNV list from the local directory through a 'Path', now supports to read data in working environment by checking the type of input file;
2. Support to return the CNVR list to working environment.

2. Update cnv_clean.R …

1. Support to return Clean CNV List to working environment.

3. Update cnv_visualising.R …

1. Support to load CNV List from working environment.

4. Update compare_cnvr.R …

1. Add new function to generate the Unique and Mutual CNVRs by uniting the overlapped CNVRs between two results. There are two purposes for this work, one is to better understand the overlapping CNVRs, the other is to mark the common regions on CNVR distribution map;

5. Update 'cnvr_plot' …

1. Add 'overlap_cnvr' argument to support to mark overlapped region on CNVR distribution map;
2. Add 'label_prop' argument to show the proportion of CNVRs length to total length of relative chromosome on CNVR map;
3. Add 'chr_col' argument to customize the color of Chromosome;
4. Add 'overlap_col' argument to customize color of overlapped CNVRs
5. Reduce the margin of final CNVR distribution map.

6. Update compare_gene.R …

1. Add 'color_label' argument to display the color of genes that passed common threshold in the Heatmap;

The First Version of HandyCNV

What's New

The first version of HandyCNV.

Range of application

Post-analysis of CNV and ROH detected from SNP genotyping data. Each function does not limit the number of chromosomes, theoretically applicable to most diploid organisms. So far, it has been successfully tested in sample of 2,000 Bovine 150K SNP chip.

Main feature

An one-stop analysis that integrates the summary, annotation, conversion, comparison and visualization, the custom input arguments and verbose outputs will help the users to identify the most interesting genome regions.