marge 0.0.3

  • completely reworked how marge checks for HOMER installation -
    • Uses options('homer_path') to hold the installation base path
    • Tries the default (e.g. if HOMER is a part of $PATH) first, susses out HOMER base
    • Failing that, asks for user to manually set it, and provides code to set in .Rprofile
    • Instructions encoded into messages following success/failure
  • added an onAttach.R to check for proper HOMER install on load with link to online docs

marge 0.0.2

  • lots of little fixes for various functions, code cleanup

marge 0.0.1.9999

  • bug fix for find_motifs_genome when using a custom background - added an fdr_num argument to add number of iterations for FDR calculation (background file was being fed to -fdr as the <num> argument); set to 0 by default since runtime takes forever when set when doing denovo enrichment
  • reads in new fdr field for denovo results, as the fdr arg for find_motifs_genome has now been enabled by default always
  • bug fix for find_motifs_genome - motif_length arg was only using the first number
  • added find_motifs_instances function to get where specific motifs (based on PWM) occur in peaks
  • added write_pwm function to support find_motifs_instances
  • created new datafile HOMER_motifs which includes all motifs used by HOMER - includes their PWMs, organism/motif set definition info
  • removed placeholder functions [read|write]_bed that were initially included for testing
  • added a new vignette

marge 0.0.1

  • initial release of marge which includes the most basic utilities needed for analysis (see below)
  • find_motifs_genome - runs motif analysis using HOMER; creates a HOMER results directory
  • read_denovo_results - reads the homerMotifs.all.motifs file created in the HOMER results directory
  • read_known_results - reads the knownResults.txt file created in the HOMER results directory