GALLO v1.5
- The functions to create the symmetric squared matrices for gene-level p-value and number of effective markers estimation were updated using sparse matrices to increase efficiency
- A new function to estimate gene-level p-values, based on Davies algortihm, was implemented
GALLO v1.4
- A new method to split the extra_info column from gff of Animal QTLdb was implemented. Therefore, the output of QTL annotation contains all the fields available in the extra_info column.
- The bug present was the end coordinates were bigger than the start coordinates were fixed. Now, GALLO automatically checks for these patterns and switches the coordinates.
- A new function to estimate gene-level p-values was implemented using a Weighted Z-score approach and Meta-analysis with LD correlation coefficients approaches
- A new function to estimate the number of independent markers using an adaptation of the simpleM method was implemented
- A new function to estimate the number of independent segments per chromosome based on the effective population size was implemented
- A new function to compute multi-trait test statistics for pleiotropic effects using summary statistics from association tests was implemented
- A new function to represent the association between two groups of variables in a dynamic network was implemented
- A new function to compute the centrality metrics for the nodes composing the network generated by the NetVis function was implemented
GALLO v1.3
- The bug resulting in the switch between the values in the column breed was fixed
GALLO v1.2
In this version the following updates were included:
- The bug resulting in the switch between the values in the columns Flank_markers and breed was fixed
- The proper citation for GALLO now can be obtained using the command citation("GALLO"")
GALLO v1.1
In this version the following updates were included:
- Inclusion of a match.arg function for the marker argument in the find_genes_qtls_around_markers function.
- The code to allow multithreading was updated in order to allow the user to choose one (1) thread as input.
- The inclusion of the argument horiz in the plot_qtl_info() function, which allow the user to choose if the legend will be plotted vertically or horizontally.
- Changes in the legend and plot area in the QTLentich_plot function in order to better address cases where the there is a large difference between the minimum and maximum number of QTLs annotated.
GALLO v0.0-99