| aggregate_roc | make aggregated roc curve |
| alt_in_cis | grab edges from walk |
| AND | test boolean AND across multiple vectors |
| appendEnv | appendEnv |
| asdf | coerce to data frame |
| asdt | coerce to data table via setDT |
| asm | asm |
| asn2 | version of utils::assignInNamespace |
| ave3 | modification of ave |
| aved | modification of ave |
| bcfindex | bcfindex |
| bedpe2grl | bedpe2grl |
| behomology | breakend exact homology |
| binom.conf | Get confidence intervals around fractions |
| bool | Clean Up Boolean Logic |
| bp2grl | convert table of paired string coordinates to GRangesList |
| cenv | concatenate environments |
| check_lst | checking list for elements that are errors checking a list... |
| classystat | calculates various scores from actual classes and predicted... |
| clobber | same as dplyr::coalesce |
| coalesce | same as dplyr::coalesce, khtools:coalesce is an alias for... |
| col2rn | alias for column_to_rownames |
| colexists | find out if column is in data.table |
| colnames2 | robust colnames |
| colnames2-set | robust colnames() assignment |
| column_to_rownames | making column into rownames |
| complete.cases2 | complete.cases wrapper |
| conform_si | conform_si |
| copy | make deep copy, recursively |
| copy2 | make deep copy |
| copy3 | make deep copy, recursively |
| copydt | copy data frame/table columns to a new data table with forced... |
| copyr6 | make deep copy of all non-function public and private fields... |
| copys4 | make deep copy of all private slots in s4 object |
| dcast.count | dcast.count |
| dcast.count2 | Counts up occurrences from a melted table |
| dcast.wrap | wrapper around dcast or dcast2 |
| debug.s4 | debug an S4 function |
| dedup | dedup |
| dedup.cols | applies dedup to colnames |
| df2gr | data frame to GRanges |
| df2grl | data frame to GRangesList |
| dg | alias of dynget |
| dig_dir | dig into a file path's directory |
| dig_dir2 | dig into a file path's directory |
| diginjob | Dig into inputs Flow Job that generated an output |
| digjob | Dig into Flow Job that generated an output |
| dig_job | Dig into Flow Job that generated an output |
| DIM | NROW and NCOL convenience function |
| DIM2 | extending NROW and NCOL2 |
| dir2 | dir with full grep |
| dirfind | Dig into outdir of flow job |
| do.assign | assign columns or list elements |
| do.cols | do.cols |
| dodo.call2 | dodo.call+ |
| do.pp | do caret preProcess |
| dot-filter_sv | .filter_sv |
| dot-gc | .gc |
| dt_any2lg | convert all columns to logical |
| dtapply | mclapply on a table split by a column |
| dt_empty2na | convert columns with empty character to NA |
| dt_f2char | convert factor columns to character |
| dt_lg2int | logical to integer in data tables |
| dt_na2empty | convert columns with NA to empty character |
| dt_na2false | convert columns with NA to false |
| dt_na2true | convert columns with NA to true |
| dt_na2zero | convert columns with NA to zeros |
| dt_setallna | convert all data.table entries to NA |
| dt_setchar | convert column to character |
| dt_setint | convert column to integer |
| dt_setnull | set columnn to NULL in data.table |
| dunlist2 | unlist into a data.table |
| duped | duped |
| dynget | modification of base::dynGet() |
| empty2na | Set vector to NA |
| enframe | same as tibble::enframe |
| enframe_list | data table-ize list elements and add name column |
| eNROW | does vapply NROW |
| errr | turn on verbose error tracing through call stack |
| est_snv_cn | estimate snv cn |
| est_snv_cn_stub | estimate snv cn stub |
| et | shortcut for eval(parse(text = <string>)) |
| extract_ggplot | helper function to grab relevant ggplot_build outputs |
| ez_string | don't use this. use base::dput() |
| f2int | factor to integer |
| false2na | replace FALSE with NA |
| feature_importance | feature_importance |
| file.exists2 | slightly more robust test for whether file exists |
| file.info2 | file.info2 |
| file.mat.exists | file.mat.exists |
| file.not.exists | slightly more robust test for whether file does not exist |
| fillby | fill in variables of data table by combos |
| find_dups | find all duplicates in a vector |
| findov | GenomicRanges::findOverlaps wrapper |
| fit_classifier | fit classiifer |
| fit.cnv.sig | fit battenberg copy number to CN signatures (Nature 2022) |
| fitcvglmnet | fit cv.glmnet |
| fitglmnet | fit glmnet |
| fitrandomforest | fit randomForest |
| fitzscore | calculate z score |
| fix.cols | Fix messed up data frame/table column names |
| flag2int | convert bam flag to integer |
| force2 | force with a tryCatch |
| forceall | force objects (including functions) to evaluate from... |
| forcefun | force functions to load |
| forceload | force functions to load from all libraries |
| frac | calculate fraction |
| g | alias for getdat2 |
| g2 | alias for getdat2 |
| gbar.error | barplot with errorbars |
| gd | alias for getdat |
| get_accuracy | calculate accuracy based on contingency table |
| getbp | get breakpoints |
| getcache | getcache |
| getdat | a method to get the "data" argument from a with/within... |
| getdat2 | getdat2 |
| get_pred | get_pred |
| gg.hist | generate ggplot histogram |
| ggmroc | ggplot for multiROC |
| gg_mytheme | custom theme for ggplot |
| gg.sline | wrapper around geom_point and geom_smooth |
| glm.nb2 | glm.nb2 |
| glmnet_aic | glmnet_aic |
| globasn | assign an object to global environment |
| good.file | Does File exists and is file size greater than threshold |
| gr2bed | gr2bed |
| gr2df | granges to datatable via dataframe |
| grabcov | convenience function to pull out coverage data from table |
| grabggtrack | convenience function to pull out jabba model + coverage |
| grabhjab | convenience function to pull out jabba model with allelic cn |
| grab.hrdetect.features | grab hrdetect features from hrdetect results |
| grapes-equals-grapes | test if two vectors are equal (uses conversion to character) |
| grapes-inn-grapes | x %inn% table a logical vector Same as |
| grapes-K-grapes | similar to setkey except a general use utility |
| grapes-nin-grapes | not x %nin% table Not match |
| grapes-Q-grapes | query |
| grapes-Q-grapes-.CompressedGRangesList | query on CompressedGRangesList |
| grapes-Q-grapes-.GRanges | query on GRangesList |
| grapes-Q-grapes-.GRangesList | query on GRangesList |
| gr_calc_cov | output data structure for ski slope from anchorlifted SNV |
| gr_construct_by | adding on by field to seqnames for more efficient by queries |
| gr_deconstruct_by | removing by field and random string barcode to seqnames for... |
| gr.disjoin | updated gr.disjoin from gUtils to work with GRangesList |
| grep_col_sort | grep_col_sort |
| grep_order | grep_order |
| gr.fixseq | get permissive seqlengths from multiple GRanges-like objects |
| gr.flipstrand | works with GRangesLists |
| gr.genome | create GRanges of full genome coordinates |
| grg_sub | extract portions of matched substring |
| grl2bedpe | grl2bedpe |
| grl.disjoin | disjoin on grangeslist |
| grl.flip | flip each GRangesList element |
| grl.flipstrand | flip strand of grangeslist |
| grl_gaps | gaps on GRangesList |
| grl.undf | grangeslist to data table via dataframe |
| gr.noval | get rid of mcols on GRanges/GRangesLists |
| grok_vcf | modded grok_vcf |
| gr.order | order granges, grangeslist |
| gr.patch | same as gr.fix basically |
| gr.resize | Resize granges without running into negative width error |
| gr.round | round window to nearest unit |
| gr.setdiff2 | gr.setdiff that works with multiple by columns |
| gr.sort | sort granges, grangeslist |
| gr.splgaps | gaps on GRanges, splitting by values in a metadata field |
| gr.split | split a gr by field(s) in elementMetadata of GRanges or a... |
| gr.sprange | get range based on a field(s) to split by in elementMetadata... |
| gr.spreduce | reduce based on a field(s) to split by in elementMetadata of... |
| gr.strand | specify strand of granges or grangeslist |
| gr.sub2 | Substitute chr in GRanges or GRangesList |
| gr_within | within on GRanges |
| gr.within | within on GRanges, S3 |
| gt.each | convenience function to plot each element separately |
| gt.fix | fix gtrack metadata elements for plotting |
| gw_edges | pull edge metadata from gwalk |
| gx | alias for getdat2(nm = "x") |
| iderr | returns ids of list elements that are errors |
| idj | idj |
| integer_breaks | make integer breaks on axes |
| interaction2 | interaction but orders levels based on input vectors |
| interbp_dist | interbp_dist |
| intercalate | collate two vectors together interleave vectors together |
| intercalate_lst | collate lists together |
| is.empty | test if object is empty |
| isNA | is.na but also tests for "NA" character |
| isv2grl | isv2grl |
| ix_sdiff | subset out indices |
| jitter2 | jitter with consistent seed |
| kcpdf | open Cairo pdf device with defaults |
| kpdf | open pdf device with defaults |
| kpng | open png device with defaults |
| ksvg | open svg device with defaults |
| lapply_dt | Flexibly apply function to columns of data.table/frame |
| lbl.gg | convenience function to label the nodes and edges of gGraph |
| len | similar to length except gets nrows for those items that have... |
| lens | similar to lengths except gets nrows for those items that... |
| levelsinuse | get the levels in use in a factor |
| lg2f | logical to factor |
| log10p | log10(x + 1) |
| loop_grep | wraps grep in for loop |
| loop_grepl | wrapper around loop_grep |
| lst.empty | lst.empty A logical vector to select which list elements are... |
| lst.empty2na | empty list elements set to NA |
| lst.empty2null | empty list elements set to NULL |
| lst.empty2replace | length 0 elements of list to replace with a value set empty... |
| lst.empty2zero | Convert empty elements to zero. |
| lst.emptychar2na | empty character elements of list to NA |
| lst.emptychar2null | empty character elements of list to NULL |
| lst.null2na | NULL elements of list to NA |
| lst.zerochar2empty | zero length character elements to empty char set 0 length... |
| main | wrapper around cenv |
| make_chunks | make_chunks |
| make_dummy | make table of dummy encodings |
| make_roc | make_roc |
| make_roc2 | make_roc2 |
| make_ttsplit | make training/test splits |
| make_xfold | make training/test splits |
| match | similar to setkey except a general use utility |
| match2 | matches x in terms of y |
| match3 | similar to setkey except a general use utility |
| match_s | ordered match |
| matrify | take a data.table/frame, shave first column into rownames,... |
| matrify2 | create matrix from table like obj with dplyr syntax |
| max.col.narm | maximum column per row (removing NA) |
| merge.repl | merging data tables with collapsing columns with the same... |
| metanames | metanames |
| min.col.narm | minimum column per row (removing NA) |
| mkst | MaKe STring making string out of vector for eval(parse(text =... |
| mrocdat | create a data frame for ggplotting multiroc |
| mroclab | create one hot table of labels for multiROC |
| mrocpred | format predicted scores for multiROC |
| mstrsplit | make matrix out of stringsplitted character vector |
| mylambdas | mylambdas |
| na2empty | na2empty A convenience function to set a character vector... |
| na2false | replace logical vector with NA to FALSE |
| na2true | replace logical vector with NA to TRUE |
| na2zero | na2zero A convenience function to set a numeric vector with... |
| names2 | robust name() |
| names2-set | robust name() assignment |
| nan2zero | nan2zero A convenience function to set a numeric vector with... |
| na.seql | NA out seqlevels |
| NCOL2 | extending NCOL |
| ne | "no error" |
| ne.na | mark x with NA if it does not exist |
| nodim | testing if object is empty |
| nonacol | no columns named "NA" |
| nonzero2na | replace 0 to with NA |
| normpath | normalize directory, but not basepath |
| normv | normalize a vector |
| normv_sep | normalize a vector, treating positives and negatives... |
| nott | negate a function |
| numeq | test equality between numeric values with some tolerance |
| off_diag | get off diagonal values |
| one_vs_other | one level vs other |
| OR | test boolean OR across multiple vectors |
| output_cols | output the union columns from a Flow output |
| overwritefun | overwrite a function in its namespace |
| overwriteR6 | overwrite a method in R6 class generator |
| pairs.collect.junctions | collect junctions from pairs as breakpoints |
| pairs.grab.hrdetect.features | grab hrdetect features from pairs table |
| pairs.grab.ot.features | grab oneness twoness features from pairs table |
| parasn | assign parallel columns |
| parse.gr2 | a robust parse.gr |
| parse.grl2 | a robust parse.grl |
| parse_slurm_time | Parse the slurm times into an R format |
| parsesnpeff | parse snpeff output into granges |
| peepr6 | peepr6 |
| pg_mytheme | print gg_mytheme output |
| pinch | pinch a vector |
| pinch.frac | pinch a vector |
| ppdf | kevin's modification of ppdf |
| ppng | kevin's modification of ppng |
| predict.pp | predict preProcess |
| printerr | print error message from tryCatch |
| process_tbl | flexibly read in a field and append an id to the output |
| qmat | query a matrix with nonmatching entries as NA |
| qq | get actual quantile values of vector |
| qtrim | cut off vector by quantiles |
| ra.dedup6 | ra.dedup6 |
| rand.string | make a random string |
| ra.overlaps6 | ra.overlaps6 |
| read.bam.header | read.bam.header |
| read_bed | read bed or bedpe as a table |
| read.header | read header of file |
| readin | flexible file opening |
| readinfasta | wrapper around readDNAStringSet to remove extraneous... |
| read_vcf2 | read_vcf2 |
| reassign | reassign elements of named list into environment |
| refactor | refactor |
| rematch | rematch |
| rep_each | recycle vector - shortcut for rep(x, each = each) |
| replace2 | function to replace elements of vector, can use "x" as... |
| replace_na | replace NAs |
| rep_len | recycle vector - overload base::rep_len |
| rep_len2 | recycle vector along length OR nrow of object |
| reset.job | reset.job |
| ret_err | a wrapper around check_lst |
| ret_na_err | using check_lst to return |
| ret_no_err | a wrapper around check_lst |
| rg_sub | extracting substring match using regexpr |
| rintersect | Reduce intersect |
| rleseq | numbers up within repeating elements of a vector |
| rmcol | rmcol |
| rm_mparen | utility function for removing multiple parantheses |
| rn2col | alias for rownames_to_column |
| robust.scale | flatten outliers by quantile |
| rownames2 | robust rownames |
| rownames2-set | robust rownames() assignment |
| rownames_to_column | making column out of rownames |
| rows.all | test whether all row entries are TRUE |
| rows.any | test whether any row entries are TRUE |
| row.sort | sort rows of integer matrix |
| rrrepeated | Recursively repeat a function call |
| runion | Reduce union |
| sampler | sample elements of vector or rows of table |
| save.r | save R data session |
| seevar | see variables in environment |
| select.matrix | select.matrix |
| selfname | name a character vector to itself |
| seq_along2 | seq along either row of table or length of vector |
| setAllNames | setAllNames convenience function to set all names of a vector |
| setcolnames | convenience function to set column names alias of setColnames |
| setColnames | convenience function to set column names |
| setcols | convenience function to set columns sets columns of an object |
| setNames2 | setNames2 convenience function to set all names of a vector |
| set_rngseed | set random number generator AND seed |
| setrownaes | convenience function to set row names sets rownames of an... |
| setRownames | convenience function to set row names sets rownames of an... |
| shift_down | shift_downstream from plyranges package |
| shift_left | shift_left from plyranges package |
| shift_right | shift_right from plyranges package |
| shift_up | shift_upstream from plyranges package |
| silent | run expression without any printed output |
| sim.bx | simulate 10x Barcoded reads off of collection of walks |
| softmax | calculate softmax |
| somejit | add tiny jitter |
| split_by | split data frame-like object based on columns |
| ss | same as subset2 |
| sstat | Kevin's implementation of sstat |
| stack.dt | collapse a named list of vectors into a data.table |
| stackenv | stackenv |
| stackenv2 | stackenv2 |
| subgr | subgr |
| subset2 | function to subset on a variable by using "x" as surrogate... |
| summ_glm | tabular summary of glm model coefficients |
| sv_filter | filter sv by overlaps with another |
| symdiff | data.table of all setdiff items in X and in Y gives back data... |
| system3 | modified system2 |
| table2 | wrapper around table(), show NA counts if there are any |
| table3 | wrapper around table, always show NA counts |
| tailf | modification of tailf from skitools |
| trans | transpose a list |
| trans.df | transpose data.table or data.frame |
| transp | transpose a list |
| try2 | wrapper around tryCatch - robust to parallel:: functions |
| un | shortcut to check unique entries |
| uncut | get upper and lower bounds of cut labels |
| undebug.s4 | undebug an S4 function |
| undup | an alternative to base::unique() that preserves names |
| unI | remove "AsIs" from class, i.e. undo I(obj) undo I(obj) |
| uniqf | Unique factor |
| upset2 | wrapper around UpSetR::upset() |
| vcf_remove_sample | take vcf read in chunks and write clean vcf |
| viewtask | convert job task to table |
| vmatch | make list of matches and nonmatches |
| whicherr | same as iderr |
| withv | withv |
| withx | withx |
| w.quantile | weighted quantile |
| write_bed | write bed or bedpe into canonical formatted table |
| write.ctab | writing a comma separated table with quotes |
| ws2und | Clean up whitespace from columns of data.frame-like object |
| wv | alias for withv |
| zscore | zscore a numeric vector |
