void bigWigCorrelateList(char *listFile)
/* Correlate all files in list to each other */
{
char **fileNames = NULL;
int fileCount = 0;
char *buf = NULL;
readAllWords(listFile, &fileNames, &fileCount, &buf);
int i;
for (i=0; i<fileCount; ++i)
{
char *aPath = fileNames[i];
char aName[FILENAME_LEN];
if (rootNames)
splitPath(aPath, NULL, aName, NULL);
else
safef(aName, sizeof(aName), "%s", aPath);
int j;
for (j=i+1; j<fileCount; ++j)
{
char *bPath = fileNames[j];
char bName[FILENAME_LEN];
if (rootNames)
splitPath(bPath, NULL, bName, NULL);
else
safef(bName, sizeof(bName), "%s", bPath);
struct correlate *c = bigWigCorrelate(aPath, bPath);
printf("%s\t%s\t%g\n", aName, bName, correlateResult(c));
correlateFree(&c);
}
}
}
void doBigWigReplicate(struct sqlConnection *conn, struct edwAssembly *assembly,
struct edwFile *elderEf, struct edwValidFile *elderVf,
struct edwFile *youngerEf, struct edwValidFile *youngerVf)
/* Do correlation analysis between elder and younger and save result to
* a new edwQaPairCorrelation record. Do this for a format where we have a bigWig file. */
{
if (pairExists(conn, elderEf->id, youngerEf->id, "edwQaPairCorrelation"))
return;
char *enrichedIn = elderVf->enrichedIn;
if (!isEmpty(enrichedIn) && !sameString(enrichedIn, "unknown"))
{
struct genomeRangeTree *targetGrt = genomeRangeTreeForTarget(conn, assembly, enrichedIn);
/* Get open big wig files for both younger and older. */
char *elderPath = edwPathForFileId(conn, elderEf->id);
char *youngerPath = edwPathForFileId(conn, youngerEf->id);
struct bbiFile *elderBbi = bigWigFileOpen(elderPath);
struct bbiFile *youngerBbi = bigWigFileOpen(youngerPath);
/* Figure out thresholds */
double elderThreshold = twoStdsOverMean(elderBbi);
double youngerThreshold = twoStdsOverMean(youngerBbi);
/* Loop through a chromosome at a time adding to correlation, and at the end save result in r.*/
struct correlate *c = correlateNew(), *cInEnriched = correlateNew(), *cClipped = correlateNew();
struct bbiChromInfo *chrom, *chromList = bbiChromList(elderBbi);
struct bigWigValsOnChrom *aVals = bigWigValsOnChromNew();
struct bigWigValsOnChrom *bVals = bigWigValsOnChromNew();
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
addBwCorrelations(chrom, targetGrt, aVals, bVals, elderBbi, youngerBbi,
elderThreshold, youngerThreshold, c, cInEnriched, cClipped);
}
/* Make up correlation structure . */
struct edwQaPairCorrelation *cor;
AllocVar(cor);
cor->elderFileId = elderVf->fileId;
cor->youngerFileId = youngerVf->fileId;
cor->pearsonOverall = correlateResult(c);
cor->pearsonInEnriched = correlateResult(cInEnriched);
cor->pearsonClipped = correlateResult(cClipped);
edwQaPairCorrelationSaveToDb(conn, cor, "edwQaPairCorrelation", 128);
bigWigValsOnChromFree(&bVals);
bigWigValsOnChromFree(&aVals);
genomeRangeTreeFree(&targetGrt);
freez(&cor);
correlateFree(&c);
bigWigFileClose(&youngerBbi);
bigWigFileClose(&elderBbi);
freez(&youngerPath);
freez(&elderPath);
}
}
double correlateArrays(double *x, double *y, int size)
/* Return correlation of two arrays of doubles. */
{
struct correlate *c = correlateNew();
double r;
int i;
for (i=0; i<size; ++i)
correlateNext(c, x[i], y[i]);
r = correlateResult(c);
correlateFree(&c);
return r;
}
double correlatePair(struct metaWig *a, struct metaWig *b)
/* Correlate a pair of metaWigs. */
{
struct correlate *c = correlateNew();
struct slName *chrom, *chromList = metaWigChromList(a);
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
struct lm *lm = lmInit(0);
struct bbiInterval *aList = metaIntervalsForChrom(a, chrom->name, lm);
struct bbiInterval *bList = metaIntervalsForChrom(b, chrom->name, lm);
verbose(2, "%s a(%d) b(%d)\n", chrom->name, slCount(aList), slCount(bList));
sortedApplyOverlapping(aList, bList, slListNextWrapper,
bbiIntervalCmpEnd, bbiIntervalOverlap, bbiIntervalCorrelatePairWrapper, c);
lmCleanup(&lm);
}
slFreeList(&chromList);
double result = correlateResult(c);
verbose(2, "correlate: r %g, sumX %g, sumY %g, n %lld\n", result, c->sumX, c->sumY, c->n);
correlateFree(&c);
return result;
}
double chromGraphBinCorrelate(char *aFile, char *bFile)
/* Do correlation between two graphs. */
{
struct chromGraphBin *a = chromGraphBinOpen(aFile);
struct chromGraphBin *b = chromGraphBinOpen(bFile);
struct cgbChrom *chrom;
struct correlate *c = correlateNew();
double r;
for (chrom = a->chromList; chrom != NULL; chrom = chrom->next)
{
chromGraphBinSeekToChrom(a, chrom->name);
if (chromGraphBinSeekToChrom(b, chrom->name))
{
correlateChrom(a, b, c);
}
}
r = correlateResult(c);
correlateFree(&c);
return r;
}
void doBigBedReplicate(struct sqlConnection *conn, char *format, struct edwAssembly *assembly,
struct edwFile *elderEf, struct edwValidFile *elderVf,
struct edwFile *youngerEf, struct edwValidFile *youngerVf)
/* Do correlation analysis between elder and younger and save result to
* a new edwQaPairCorrelation record. Do this for a format where we have a bigBed file. */
{
/* If got both pairs, work is done already */
if (pairExists(conn, elderEf->id, youngerEf->id, "edwQaPairSampleOverlap")
&& pairExists(conn, elderEf->id, youngerEf->id, "edwQaPairCorrelation"))
return;
int numColIx = 0;
if (sameString(format, "narrowPeak") || sameString(format, "broadPeak"))
numColIx = 6; // signalVal
else
numColIx = 4; // score
numColIx -= 3; // Subtract off chrom/start/end
char *enrichedIn = elderVf->enrichedIn;
struct genomeRangeTree *targetGrt = NULL;
if (!isEmpty(enrichedIn) && !sameString(enrichedIn, "unknown"))
targetGrt = genomeRangeTreeForTarget(conn, assembly, enrichedIn);
/* Get open big bed files for both younger and older. */
char *elderPath = edwPathForFileId(conn, elderEf->id);
char *youngerPath = edwPathForFileId(conn, youngerEf->id);
struct bbiFile *elderBbi = bigBedFileOpen(elderPath);
struct bbiFile *youngerBbi = bigBedFileOpen(youngerPath);
/* Loop through a chromosome at a time adding to correlation, and at the end save result in r.*/
struct correlate *c = correlateNew(), *cInEnriched = correlateNew();
struct bbiChromInfo *chrom, *chromList = bbiChromList(elderBbi);
long long elderTotalSpan = 0, youngerTotalSpan = 0, overlapTotalSpan = 0;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
addBbCorrelations(chrom, targetGrt, elderBbi, youngerBbi, numColIx, c, cInEnriched,
&elderTotalSpan, &youngerTotalSpan, &overlapTotalSpan);
}
/* Make up correlation structure and save. */
if (!pairExists(conn, elderEf->id, youngerEf->id, "edwQaPairCorrelation"))
{
struct edwQaPairCorrelation *cor;
AllocVar(cor);
cor->elderFileId = elderVf->fileId;
cor->youngerFileId = youngerVf->fileId;
cor->pearsonOverall = correlateResult(c);
cor->pearsonInEnriched = correlateResult(cInEnriched);
edwQaPairCorrelationSaveToDb(conn, cor, "edwQaPairCorrelation", 128);
freez(&cor);
}
/* Also make up sample structure and save. */
if (!pairExists(conn, elderEf->id, youngerEf->id, "edwQaPairSampleOverlap"))
{
struct edwQaPairSampleOverlap *sam;
AllocVar(sam);
sam->elderFileId = elderVf->fileId;
sam->youngerFileId = youngerVf->fileId;
sam->elderSampleBases = elderTotalSpan;
sam->youngerSampleBases = youngerTotalSpan;
sam->sampleOverlapBases = overlapTotalSpan;
setSampleSampleEnrichment(sam, format, assembly, elderVf, youngerVf);
edwQaPairSampleOverlapSaveToDb(conn, sam, "edwQaPairSampleOverlap", 128);
freez(&sam);
}
genomeRangeTreeFree(&targetGrt);
correlateFree(&c);
bigBedFileClose(&youngerBbi);
bigBedFileClose(&elderBbi);
freez(&youngerPath);
freez(&elderPath);
}
