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topr 2.0.2

• Parameters added for downsampling/thinning the dataset prior to plotting with manhattan
• Locuszoom plot updated to include variants with missing R2 values
• vline_color bug fix
• Improved get_lead_snp functionality
• The get_sign_and_sugg_loci function added for extracting genome-wide significant and suggestive loci
• The manhattanExtra function added for highlighting genome-wide significant and suggestive loci

topr 2.0.1

• REF and ALT error message fixed when there are p-values below .Machine$double.xmin in the input dataset
• The limits= argument added in the scale_color_manual ggplot2 function for it to work as expected with ggplot2 v3.5

topr 2.0.0

• topr can now be used with any species
• argument added to set the color of the diagonal line in qqtopr
• Argument chr_ticknames, show_all_chrticks, hide_chrticks_from_pos, hide_chrticks_to_pos and hide_every_nth_chrtick added to the Manhattan function to control x-axis labels
• The log_trans_p argument was added for input datasets that have already been log-transformed
• Inclusion of chromosomes Y and MT in build hg38

topr 1.1.10

• Argument get_chr_lengths_from_data added to the Manhattan function so the number of chromosomes and chromosome lengths can be extracted from the input data.
• The Manhattan plot displays as many chromosomes as are in the input data.

topr 1.1.9

• Correct gene annotation used in regionplot when using build 37
• Fix of partly incorrect coloring of association points near the end or beginning of a chromosome.

topr 1.1.8

• Missing shade added for chr22 on Manhattan plot when chrX is not included in the dataset.

topr 1.1.7

• Placeholder added when there are no genes in the region on display
• Fix for the manhattan function to handle one chromosome datasets
• xaxis_label added as an input argument to the manhattan plot function

topr 1.1.6

• Updated documentation

topr 1.1.5

• Fix for chrX when displaying genes in regionplot

topr 1.1.4

• Default significance threshold changed from 5e-9 to 5e-8
• Updated README

topr 1.1.3

• Fix to make topr compatible with the next version of dplyr

topr 1.1.2

• the scale parameter for annotate_with_vline was fixed
• the Manhattan plot was changed to the more conventional two-color display
• the argument theme_grey can be set to TRUE to make the Manhattan plot look like it does in older versions of topr

topr 1.1.1

• Minor bug fix for plot colors and legends when plotting multiple datasets
• region argument added to the manhattan function

topr 1.1.0

• Update to increase control over plot aesthetics and variant labeling
• minor bug fixes
• Includes the option to choose between genome builds 38 (GRCh38.p13) and 37 (GRCh37.p13).

topr 1.0.0

• First official release of topr

topr 0.0.1

• First version including locuszoom plot

topr 0.0.0

• First version submitted to github

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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