Man pages for greymonroe/polymorphology
Functions from Monroe et al 2022
| contexts | trinucleotide context |
| contexts_plot | plot trinucleotide context |
| extract_epigenome | Extract values for epigenomic features in a given region.... |
| getTajimasD | extract Tajimas D for features |
| ggplot_tss | ggplot_tss |
| homopolymer_context | homopolymer_context |
| Null_ns_s | get estimate null nonsynonymous/synonymous ratio |
| parse_vcf | parse through vcf file so it can be used in R |
| region_counts | add counts of variants to gff data object |
| tss_means | tss_means |
| tss_tts.calc | calculate minor allele frequencies of polymorphisms in... |
| tss_tts.feature | extract relative position of polymorphisms in relation to... |
| tss_tts.maf | calculate minor allele frequencies of polymorphisms in... |
| tss_tts.mappability | extract relative position of polymorphisms in relation to... |
| tss_tts.tajima | extract relative position of polymorphisms in relation to... |
| tss_tts.tajima.plot | plot relative position of tajimas D in relation to gene... |
| tss_tts.variants | extract relative position of polymorphisms in relation to... |
| tss_tts.variants.plot | plot relative position of polymorphisms in relation to gene... |
| variant_features | annotate variants with features from gff |
