e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/microarray.h src/hg/inc/microarray.h index 5630086..72eb7ab 100644 --- src/hg/inc/microarray.h +++ src/hg/inc/microarray.h @@ -1,200 +1,203 @@ /* Microarray code common to hgc, hgTracks, and hgNear. */ /* Also use in loaders like hgRatioMicroarray and hgMedianMicroarray. */ +/* Copyright (C) 2011 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef MICROARRAY_H #define MICROARRAY_H #ifndef EXPRECORD_H #include "expRecord.h" #endif #ifndef CART_H #include "cart.h" #endif #ifndef BED_H #include "bed.h" #endif #ifndef TRACKDB_H #include "trackDb.h" #endif #ifndef CUSTOMTRACK_H #include "customTrack.h" #endif #define MICROARRAY_MISSING_DATA -10000 /* This is an important constant. Often zero and negative numbers are valid */ /* microarray data. -10000 is often used then. */ /* Just an enum to list the several ways of combining columns of data. */ enum maCombineMethod { useMedian = 0, useMean = 1, }; /* Enum to use list the types of ways to color the microarray */ enum expColorType { redGreen = 0, redBlue = 1, yellowBlue = 2, redBlueOnWhite = 3, redBlueOnYellow = 4, }; double maDoubleMeanHandleNA(int count, double *array); /* Calculate the mean value of an array, skipping the NA vals. */ double maDoubleMedianHandleNA(int count, double *array); /* Return median value in array, skipping the NAs. */ struct maMedSpec /* A specification for median. */ { struct maMedSpec *next; char *name; /* Column name. */ char *group; /* Tissue/group name. */ int count; /* Count of experiments to median. */ int *ids; /* Id's (indexes) of experiments to median. */ }; struct maMedSpec *maMedSpecReadAll(char *fileName); /* Read in file and parse it into maMedSpecs. */ struct expData *maExpDataGroupByExtras(struct expData *exps, struct expRecord *erList, int extrasIndex, enum maCombineMethod method, int minExps); /* Combine experiments using mean or median and the grouping defined by the */ /* expRecord/extrasIndex combination. */ struct expData *maExpDataMeanByExtras(struct expData *exps, struct expRecord *erList, int extrasIndex, int minExps); /* Given the data, the expRecords, and the index for the grouping, mean the */ /* columns in the data. */ struct expData *maExpDataMedianByExtras(struct expData *exps, struct expRecord *erList, int extrasIndex, int minExps); /* Given the data, the expRecords, and the index for the grouping, median the */ /* columns in the data. */ struct expData *maExpDataMedianFromSpec(struct expData *exps, struct maMedSpec *specs, int minExps); /* Given the data, the and a maMedSpec list, median the columns in the data. */ int maExpDataNumBadScoresForProbe(struct expData *exps, char *probeName); /* Given a probe name, find that probe's data in the list and report */ /* the # of NA (< -9999) values in the expScores. I.e. how many bad */ /* experiments are there. Return -1 if name not found. */ int maExpDataNumBadScoresForOneArray(struct expData *exps, struct expRecord *ers, char *arrayName); /* Find # of bad datapoints for a certain column (array) in the dataset. */ /* return -1 if not found. */ float maExpDataOverallMean(struct expData *exps); /* Return the overall mean for the expression data. */ float maExpDataOverallMedian(struct expData *exps); /* Return the overall median for the expression data. */ void maExpDataClipMin(struct expData *exps, float minGood, float minVal); /* If an expData->expScores datapoint is < minGood, set it to minVal. */ void maExpDataDoLogRatioMeanOrMedian(struct expData *exps, boolean mean); /* For the M x N sized expression matrix, change each value to be the ratio */ /* of that value to the mean or median of values in that value's row (gene). */ /* This involves no clumping of experiments to calculate the median/mean. */ void maExpDataDoLogRatioTranspose(struct expData *exps, boolean mean); /* For the M x N sized expression matrix, change each value to be the ratio */ /* of that value to the mean or median of values in that value's column (probe). */ /* This involves no clumping of experiments to calculate the median/mean. */ void maExpDataDoLogRatioClumpExpRecord(struct expData *exps, struct expRecord *erList, int extrasIndex, enum maCombineMethod method); /* Log ratio the expData list. The ratio of the denominator is the median of */ /* medians or the mean of means of each group of experiments. This grouping */ /* is defined by the expRecord/extrasIndex combination. The log is base 2. */ void maExpDataDoLogRatioGivenMedSpec(struct expData *exps, struct maMedSpec *specList, enum maCombineMethod method); /* Same as maExpDataDoLogRatioClumpExpRecord except use the maMedSpec as the */ /* thing to base the groupings off of. */ void maExpDataAddConstant(struct expData *exps, double c); /* Add a constant c to all of the microarray data. Ensure that NA values */ /* aren't inadvertantly created. */ struct maGrouping /* Store the vital information for one of the "paragraphs" in the */ /* microarrayGroups.ra file. */ { struct maGrouping *next; char *name; char *type; char *description; int size; int numGroups; int *expIds; int *groupSizes; char **names; }; struct microarrayGroups /* Store all the vital info for a set of groupings in a microarrayGroups.ra */ /* file. */ { int numCombinations; int numSubsets; struct maGrouping *allArrays; struct maGrouping *combineSettings; struct maGrouping *subsetSettings; struct maGrouping *defaultCombine; }; void maGroupingFree(struct maGrouping **pMag); /* free up a maGrouping */ void maGroupingFreeList(struct maGrouping **pList); /* Free up a list of maGroupings. */ void microarrayGroupsFree(struct microarrayGroups **pGroups); /* Free up the microarrayGroups struct. */ struct microarrayGroups *maGetTrackGroupings(char *database, struct trackDb *tdb); /* Get the settings from the .ra files and put them in a convenient struct. */ struct maGrouping *maGetGrouping(struct microarrayGroups *groupings, char *name); /* Return the specfic grouping (combine or subset), or NULL if not found */ struct maGrouping *maGetGroupingFromCt(struct customTrack *ct); /* Spoof an "all" maGrouping from a customTrack. */ struct bed *ctLoadMultScoresBedDb(struct customTrack *ct, char *chrom, int start, int end); /* If the custom track is stored in a database, load it. */ struct maGrouping *maCombineGroupingFromCart(struct microarrayGroups *groupings, struct cart *cart, char *trackName); /* Determine which grouping to use based on the cart status or lack thereof. */ struct maGrouping *maSubsetGroupingFromCart(struct microarrayGroups *groupings, struct cart *cart, char *trackName); /* Determine which subsetting to use based on the cart status or lack thereof. */ int maSubsetOffsetFromCart(struct maGrouping *subset, struct cart* cart, char *trackName); void maBedClumpGivenGrouping(struct bed *bedList, struct maGrouping *grouping, struct maGrouping *subset, int subsetOffset); /* Clump (mean/median) a bed 15 given the grouping kind. */ struct maGrouping *maHashToMaGrouping(struct hash *oneGroup); /* This converts a single "stanza" of the microarrayGroups.ra file to a maGrouping struct. */ enum expColorType getExpColorType(char *colorScheme); /* From a color type return the respective enum. */ /* Linking to UI options... */ char *expRatioCombineDLName(char *trackName); char *expRatioSubsetRadioName(char *trackName, struct microarrayGroups *groupings); char *expRatioSubsetDLName(char *trackName, struct maGrouping *group); #endif