void saveDataTable(struct expData *data)
/* Create the expression table the cheesey way by loading a temp tab file. */
{
FILE *f = hgCreateTabFile(".", table);
struct expData *cur;
struct sqlConnection *conn = sqlConnect(database);
expDataCreateTable(conn, table);
for (cur = data; cur != NULL; cur = cur->next)
expDataTabOut(cur, f);
hgLoadTabFile(conn, ".", table, &f);
hgRemoveTabFile(".", table);
sqlDisconnect(&conn);
}
void hgRatioMicroarray(char *absTable, char *relTable)
/* hgRatioMicroarray - Create a ratio form of microarray. */
{
struct maMedSpec *clumpList = NULL;
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char **row;
char query[512];
struct expData *ex;
struct expData *expList = NULL;
FILE *f = hgCreateTabFile(tabDir, relTable);
int rowCount = 0;
if (clump != NULL)
clumpList = maMedSpecReadAll(clump);
sqlSafef(query, sizeof(query),
"select * from %s", absTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
ex = expDataLoad(row);
slAddHead(&expList, ex);
if (limit != 0 && rowCount >= limit)
break;
}
sqlFreeResult(&sr);
slReverse(&expList);
maExpDataClipMin(expList, minAbsVal, minAbsVal * 0.5);
maExpDataAddConstant(expList, c);
if (transpose)
maExpDataDoLogRatioTranspose(expList, doAverage);
else
maExpDataDoLogRatioGivenMedSpec(expList, clumpList, (doAverage) ? useMean : useMedian);
for (ex = expList; ex != NULL; ex = ex->next)
expDataTabOut(ex, f);
if (doLoad)
{
expDataCreateTable(conn, relTable);
hgLoadTabFile(conn, tabDir, relTable, &f);
hgRemoveTabFile(tabDir, relTable);
}
expDataFreeList(&expList);
sqlDisconnect(&conn);
}
void makeNewDataTable(char *database, char *oldTable, struct maMedSpec *medList, char *newTable)
/* Create new table in database based on medians of data
* in old table as defined by medList. */
{
struct sqlConnection *conn = sqlConnect(database);
FILE *f = hgCreateTabFile(tabDir, newTable);
struct expData *expList, *medianExpList, *exp;
expList = expDataLoadTableLimit(conn, oldTable, limit);
medianExpList = maExpDataMedianFromSpec(expList, medList, minExps);
for (exp = medianExpList; exp != NULL; exp = exp->next)
expDataTabOut(exp, f);
if (doLoad)
{
expDataCreateTable(conn, newTable);
hgLoadTabFile(conn, tabDir, newTable, &f);
hgRemoveTabFile(tabDir, newTable);
}
expDataFreeList(&expList);
expDataFreeList(&medianExpList);
sqlDisconnect(&conn);
}
