NEWS.md

In bmansfeld/QTLseqR: QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

QTLseqr 0.7.5.2

Bugs

• Import failure caused by 0.7.5.1 fixed

QTLseqr 0.7.5.1

Bugs

• Import failure caused by 0.7.5 fixed

QTLseqr 0.7.5

Bugs

• reading files would sometimes guess wrong. Set the default to col_character. This will help with very large read depth importing.

QTLseqr 0.7.4

Bugs

• Fixed a compatibility issue with new versions of the modeest package. Please note that from now on QTLseqr requires modeest (> 2.3.2)

QTLseqr 0.7.3

Updates

• Added a ... for all functions that use tricubed smoothing functions. So that users can easily pass higher maxk values to raw.locfit.
• Added "A note about window sizes" to the vignette.

QTLseqr 0.7.2

Updates

• Added depthDifference paramater to filterSNPs function. This helps filtering SNPs with high absolute differences in read depth between the bulks.
• getQTLTable now also reports the genomic position of the maximum of each peak.
• Updates to the vignette about filtering SNPs.

QTLseqr 0.7.1

Bug fixes

• Corrected a bug in checking for negative bulksizes

QTLseqr 0.7.0

Updates

• Added importFromTable function to allow users to import from a delimited file.
• Allowed different size bulks in runQTLseqAnalysis.
• Updated vignettes and documentation files.
• Some documentation link fixes

QTLseqr 0.6.5

Bug fixes

• Corrected a bug in import that happend when high or low bulks were named with things that looked like CHROM, POS, ALT or REF. Now the function ignores those columns when renaming to HIGH.xx or LOW.xx. Also better definition of column types to force CHROM to be char and POS to be int.

QTLseqr 0.6.4

Bug fixes

• Corrected a windowSize that was set to 1e6 instead of the parameter function in 'runQTLanalysis'. This was causing problems in calculating window depth.

QTLseqr 0.6.3

Bug fixes

• Corrected a call to global env variables in importFromGATK.
• Fixed issues with bulk names that had periods in them.
• Bug fix in export functions using table as variable name.

QTLseqr 0.6.2

Bug fixes

• Added responsive x axis brakes. Axis brake labels were getting squashed on small chromosomes.

QTLseqr 0.6.1

Updates

• added plotSimulatedThresholds function to help users visuallize their confisence intervals
• some manual corrections and mods

QTLseqr 0.6.0

Updates

• Added QTLseq analysis functionality
• plotQTLStats can now plot confidence intervals in $\Delta (SNP\text{-}index)$ plots
• Export functions run faster and allow for detection of QTL in either "Gprime" or "QTLseq" methods
• removed Bioconductor dependency

QTLseqr 0.5.8

Updates

• changed $\Delta SNP\text{-}index$ to $\Delta (SNP\text{-}index)$

QTLseqr 0.5.7

Updates

• plotQTLStats now allows for chromosome facet shape scaling using the 'scaleChroms' parameter

QTLseqr 0.5.6

Bug fixes

• Added package locfit to Imports.

QTLseqr 0.5.5

Updates

• plotGprimeDist null distribution label more accurate.

QTLseqr 0.5.4

Updates

• plotGprimeDist now plots histograms of filtered and raw data. overlaid with the null dist. Is easier to interpret.

QTLseqr 0.5.3

New features

• Added a NEWS.md file to track changes to the package.
• in plotGprimeDist plotting now includes density plots of all data, data after QTL filtering and the null-distribution assuming mean and variance of the filtered set.

Bug fixes

• Corrected a bug in getFDRThreshold function that was using regular p-values and not adjusted pvalues to define threshold

bmansfeld/QTLseqR documentation built on Jan. 25, 2020, 8:52 p.m.